Structurally modified COI1

ABSTRACT

Described herein are plants that are resistant to herbicides, such as herbicide compositions comprising coronatine, where the herbicide-resistant plants express a modified CORONATINE INSENSITIVE 1 (COI1) protein.

This application claims benefit of priority to the filing date of U.S. Provisional Application Ser. No. 62/413,850, filed Oct. 27, 2016, the contents of which are specifically incorporated herein by reference in their entity.

GOVERNMENT FUNDING

This invention was made with government support under AI060761 awarded by the National Institutes of Health, and under DE-FG02-91ER20021 awarded by the U.S. Department of Energy. The government has certain rights in the invention.

BACKGROUND

The protection of crops from weeds and other vegetation which inhibit crop growth is a constantly recurring problem in agriculture. To help combat this problem, researchers in the field of synthetic chemistry have produced an extensive variety of chemicals and chemical formulations effective in the control of such unwanted growth. Secondary metabolites produced by microbes have in some instances been used for weed and pest control in agricultural applications.

Plants are capable of activating a large array of defense mechanisms in response to pathogen attack, some of which are preexisting and others are inducible. In the past few years it has become apparent that jasmonic acid (JA) and salicylic acid (SA) signaling can play an important role in regulation of pathogen defenses. SA signaling and JA signaling pathways are interconnected in complicated ways. For example, some studies have shown that SA signaling and JA signaling are mutually inhibitory (Creelman et al., Annu. Rev. Plant Physiol. Plant Mol. Biol., 48:355 (1997); Gupta et al., Molec Plant-Microbe Interact 13(5): 503-511 (2000).

Pathogen infections and weeds can cause significant crop losses worldwide. Pathogens can also lead to disturbances in natural ecosystems. An understanding how plants control infections and respond to herbicides, for example via expression of defense mechanisms, can lead to new and beneficial ways to handle plant pathogens and control weed problems.

SUMMARY

Modified polypeptides, expression cassettes, modified plants, and modified seeds are described herein that are resistant to plant pathogens, including highly evolved plant pathogens and pests such as bacteria and insects. In addition, the modified polypeptides, expression cassettes, modified plants, and modified seeds described herein are resistant to herbicides.

Described herein are modified CORONATINE INSENSITIVE 1 (COI1) proteins that have amino acid sequences with at least one amino acid substitution within a jasmonate binding pocket of the modified COI1 protein relative to a native (wild type) COI1 protein amino acid sequence, wherein the at least one amino acid substitution reduces complex formation between the modified COI1 protein, coronatine, and a JAZ repressor protein as compared to the native (wild types) COI1 protein.

Expression cassettes and expression cassettes that encode and can express such modified COI1 proteins are also described herein. Cells and plants that have been modified to express such modified COI1 proteins are also described herein. The modified cells and plants can express heterologous modified COI1 proteins or the endogenous COI1 gene can be modified so that the modified COI1 protein is expressed.

Methods of making modified cells and modified plants are also described herein.

Methods are also described that involve applying an herbicide to a series of plants, to an agricultural field, or to any area where weed control is desired, where the series of plants, the agricultural field, or the area includes a modified plant that can express the modified COI1 plant. Such methods can reduce the growth, root length, and/or survival of undesired plants (e.g., weeds), while in comparison the modified plant has longer roots and grows well (better than the undesired plants or weeds).

DESCRIPTION OF THE FIGURES

FIG. 1A-1B illustrate the effects of CORONATINE INSENSITIVE 1 (COI1) alanine substitutions on COI1-JAZ9 interactions as measured by Y2H assays of protein-protein interaction, when the assays included 10 μM coronatine (COR; a JA-mimicking toxin). FIG. 1A shows interactions between JAZ9 and thirty-two different alanine-substitution COI1 mutants selected on the basis of the TIR1 crystal structure. Darker (blue) colonies indicate positive interactions, while lighter (light green) colonies indicate that COI1-JAZ9 were disrupted. As illustrated, JAZ9 interactions were reduced when COI1 had alanine substitution at M88, F89, L91, R121, E173, R348, R351, D354, G357, Y386, D407, R409, L410, V411, L412, L413, R415, R440, F443, L469, L470, Y472, Q491, K492, R496, and R516. FIG. 1B shows interactions between JAZ9 and ten additional alanine-substitution COI1 mutants selected on the basis of the COI1 crystal structure. As illustrated, JAZ9 interactions were reduced with COI1 Y302, R326, and Y444 alanine substitution mutants.

FIG. 2A-2E illustrate interactions between COI1 substitution mutants and JAZ9 under various conditions. FIG. 2A shows liquid Y2H results of JAZ9 interaction with COI1 mutants in which each of seven selected JA-Ile-contacting residues within COI1 was substituted with alanine. FIG. 2B shows liquid Y2H results of JAZ9 interaction with COI1 mutants in which each of three additional JA-Ile-interacting residues was substituted with alanine. FIG. 2C shows liquid Y2H results of JAZ9 and seven additional COI1 mutants with substitutions at the A384 position. FIG. 2D shows a Western blot for COI1 A384 substitution mutant expression in yeast, showing that A384V and other A384 substitution mutants are expressed and stable in yeast. Anti-LexA antibody was used for detection of COI1 proteins expressed from a pGilda vector and anti-HA antibody was used for detection of JAZ9 expression from pB42AD vector. RLU indicates the degree of interaction between COI1 mutants and JAZ9 in the presence of either 1 μM COR, 10 μM JA-Ile (or 30 μM JA-Ile), or 1% DMSO treatment. Different letters above columns indicate significant differences (P<0.05) between different treatments (i.e., DMSO, JAIle, or COR) for the same set of interacting proteins. For those interacting proteins that do not have letter labels above columns, no significant differences were detected between treatments. Two-way ANOVA with Bonferroni posttest was used. Data were presented as mean±SEM (A: n=2; B and C: n=3). FIG. 2E shows an alignment of amino acids of COI1 orthologs involved in ligand-receptor interaction in the ligand binding pocket where the species of the orthologs are recited at the right. The position of A86 with respect to JA-Ile and COR bound in COI1 ligand binding pocket is also shown. Fourteen amino acids involved in JA-Ile interaction in the Arabidopsis COI1 protein are shown with the corresponding amino acids in six representative plant species. Green dots below the alignment indicate amino acids contacting with JA-Ile/COR; blue dots indicate amino acids that also make contact with JAZ1; and red dots indicate amino acids that make contact with InsP5. Abbreviations: Arabidopsis thaliana (At), Solanum lycopersicum (Sl), Populus trichocarpa (Pt), Brachypodium distachyon (Bd), Picea abies (Pa), Selaginella moellendorffii (Sm), Physcomitrella patlens (Pp).

FIG. 3 illustrates structures of JA-Ile or COR in the ligand-binding site of COI1 or COI1A384V. Panels A and B illustrate the binding pose of JA-Ile (panel A) and COR (panel B) in the ligand-binding site of COI1 in the crystal structures of the COI1-JAZ1 complex (PDB ID codes 3OGL and 3OGK, respectively). Amino acid contacts in the ligand pocket were described by Sheard et al. (Nature 468(7322):400-405 (2010)). Panels C and D illustrate structures of the A384V substitution COI1 mutant showing expected steric clash with the isoleucine side-chain of JA-Ile or the ethyl group attached to the cyclopropane moiety of COR. The isoleucine side-chain of JA-Ile can be adjusted in the mutant ligand binding site by rotation of the side-chain dihedral angle, χ1 of isoleucine (panel C). In contrast, the steric clash (highlighted in red box) impairs COR binding in the ligand-binding site because the rotatable bond at the equivalent position is absent in COR (panel D). The ligand-binding site in COI1 is shown in gray-colored surface representation. Ligands and A384/V384 residues are shown in stick representation, whereas all other atoms in the protein are shown in line representation. C-atoms in the wild type and mutant COI1 proteins are shown in green and cyan, respectively; those in JA-Ile and COR are shown in yellow and magenta, respectively. In protein and ligand molecules N—, O—, and H-atoms are colored in blue, red, and gray, respectively, and, for clarity, nonpolar H-atoms are not shown. Panel E illustrates the molecular structure of JA-Ile with the χ1 torsion angle shown by the cyan arrow. Panel F illustrates the molecular structure of COR in which the cyclopropane moiety can restrict the rotational freedom of the terminal ethyl group. The cyclopropane moiety along with the ethyl substitution is highlighted in yellow.

FIG. 4A-4C shows graphs of Y2H and pull-down assay results illustrating the physical interactions between COI1 and JAZ9 proteins. FIG. 4A illustrates liquid Y2H assay results of JAZ9 interaction with mutant COI1 proteins containing amino acid substitutions at position 86 or 384 in the presence of 1 μM COR or 30 μM JA-Ile. FIG. 4B illustrates liquid Y2H results of COI1-JAZ9 interaction in the presence of different concentrations of JA-Ile and COR. Relative light units (RLU) indicated the degree of interaction between COI1 mutants and JAZ9. One-percent DMSO treatment was used as mock treatment. Different letters of the same type above columns indicate significant differences (P<0.05) between different treatments (i.e., DMSO, JA-Ile, or COR) for the same set of interacting proteins (n=3, error bars, SEM). For bar graphs that do not have letter labels above their columns, no significant differences were detected for the interacting proteins in those treatments. Two-way ANOVA with Bonferroni posttest was used for FIG. 4A. One-way ANOVA with Tukey's multiple comparison test was used for FIG. 4B. FIG. 4C illustrates results of co-receptor pull-down assays. Pulldown assays were performed with protein extracts from pCOI1:COI1WT/A384V-4×c-Myc plants and recombinant E. coli-expressed MBP-JAZ9-8×His in the presence of COR or JA-Ile at the indicated concentrations. Proteins bound to MBP-JAZ9-8×His were analyzed by immunoblotting. Anti-c-Myc antibody was used for detection of COI1WT/A384V-4×c-Myc protein. The Coomassie blue-stained gel shows the amounts of MBP-JAZ9-8×His pulled down by the Ni affinity resin.

FIG. 5A-5F illustrate the phenotypes of transgenic COI1WT and COI1A384V plants. FIG. 5A shows an image illustrating restoration of male fertility in transgenic COI1/COI1WT and COI1/COI1A384V plants. FIG. 5B illustrates COI1 protein levels in pCOI1:COI1WT-4×c-Myc and pCOI1:COI1A384V-4×c-Myc transgenic plants. Coomassie blue-stained ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCo) protein was used as loading control. FIG. 5C illustrates the quantity (percentage) of root growth in an assay in the presence of 10 μM MeJA or 0.2 μM COR. Relative root length was compared with mock treatment (0.1% DMSO). Different letters of the same type above columns indicate significant differences (P<0.05) between different plant genotypes with the same treatment (MeJA or COR) (n=15, error bars, SEM, except for COI1-30, n=7), as determined by two-way ANOVA with Bonferroni posttest. *** indicates P<0.001 significant differences between two ligand treatments of the same plant genotype (while ns: not significant). FIG. 5D illustrates the fold-changes of JAZ9 gene expression in Col-0, transgenic COI1WT, COI1A384V, and COI1-30 plants after 10 μM MeJA or 0.2 μM COR induction, relative to those in COI1-30-null plants with 10 μM MeJA. The internal control employed was the PROTEIN PHOSPHATASE 2A SUBUNIT A3 gene (PP2AA3, AT1G13320). Different letters of the same type above columns indicate significant differences (P<0.05) of gene expression between different plant genotypes with the same ligand treatment (MeJA or COR) (n=4, error bars, SEM), by two-way ANOVA with Bonferroni posttest. **P<0.01 and ***P<0.001 indicate significant differences between two different ligand treatments of the same plant genotype (ns, not significant). FIG. 5E graphically illustrates expression of the salicylic acid (SA)-responsive gene, PR1, in Col-0, COI1WT and COI1A384V plants. FIG. 5F graphically illustrates expression of the SA-responsive gene SID2 in Col-0, COI1WT, and COI1A384V plants. For the experiments providing the results in FIG. 5E-5F, PP2AA3 was used as an internal control gene, and a one-way ANOVA with Dunnett test was used (n=4, error bars, SEM). No significant difference (P<0.05) was detected in the expression levels shown in FIGS. 5E-5F.

FIG. 6A-6F illustrates the effects of bacterial infections by Pseudomonas syringae pv tomato (Pst) DC3000, Pseudomonas syringae pv maculicola (Psm) ES4326, Pseudomonas syringae pv tomato DC3118 and Pseudomonas syringae pv tomato DB29. The Pseudomonas syringae pv tomato DC3118 and Pseudomonas syringae pv tomato DB29 strains are two COR-deficient mutants of Pseudomonas syringae pv tomato DC3000. FIG. 6A illustrates the disease symptoms of Col-0, COI1-30, COI1WT and COI1A384V leaves 3 days after dip-inoculation with 1×10⁸ cfu/mL Pst DC3000. FIG. 6B illustrates the quantity of bacterial populations on Col-0, COI1-30, COI1WT and COI1A384V 3 days after dip-inoculation with 1×10⁸ cfu/mL Psi DC3000. For FIGS. 6A-6B, ***P<0.001 indicates significant difference between mutant lines and wild-type Col-0 by one-way ANOVA with Dunnett test (n=4, error bars, SEM). FIG. 6C illustrates the disease symptoms of Col-0, COI1-30, COI1WT and COI1A384V leaves 3 days after dip-inoculation with 1×10⁸ cfu/mL Pseudomonas syringae pv maculicola (Psm) ES4326. FIG. 6D graphically illustrates the quantity of bacterial populations 3 days after dip-inoculation with 1×10⁸ cfu/mL Psm ES4326. For FIGS. 6C-6D, **P<0.01 and ***P<0.001 indicate significant difference between mutant lines and Col-0 wild-type by One way ANOVA with Dunnett test (n=4, error bars, SEM). FIG. 6E graphically illustrates the quantity of bacterial populations 4 days after infection by syringe-infiltration with 1×10⁶ cfu/mL of COR-deficient P. syringae mutant Pst DC3118. FIG. 6F graphically illustrates the quantity of bacterial populations 4 days after infection by syringe-infiltration with 1×10⁶ cfu/mL of COR-deficient P. syringae mutant DB29. No significant difference (P<0.05) was detected between plant genotypes by One-way ANOVA with Dunnett test (n=4, error bars, SEM) for the data shown in FIGS. 6E-6F.

FIGS. 7A-7C illustrate the amount of insect feeding on COI1WT and COI1A384V plants. FIG. 7A graphically illustrates the average weights of 12-day-old Spodoptera exigua larvae fed on Col-0, COI1-30, COI1WT or COI1A384V plants. The symbol *** indicates a significant difference at P<0.001 in comparisons to Col-0 using One-way ANOVA with Dunnett test (n=10, error bars, SEM). No significant difference was detected in the weight of larvae reared on Col-0, COI1WT and COI1A384V L1 plants. FIG. 7B shows images of representative larvae 12 days after feeding as described for FIG. 7A. FIG. 7C shows images of Arabidopsis plants after Spodoptera exigla larvae exposure.

DETAILED DESCRIPTION

The invention relates to plants, plant cells, and seeds that express modified CORONATINE INSENSITIVE 1 (COI1) proteins. Expression of such modified COI proteins in plants provides near-normal defense responses to pathogens and pests. Additionally, the modified COI1 proteins provide resistance to the phytotoxin coronatine, which several pathogens produce as a virulence factor. Plants expressing the modified COI1 are thus rendered resistant to coronatine (COR) and to the pathogens that use coronatine as a virulence factor. As illustrated herein, coronatine can reduce plant growth and act as an herbicide, but plants expressing the modified COI1 proteins are not susceptible to reduced plant growth. Hence, described herein are plants expressing modified COI1 proteins, as well as methods of reducing growth of plants that do not express such modified COI1 proteins while cultivating plants that do express the types of modified COI1 proteins.

COI1 is an F-box protein that can mediate jasmonate signaling by promoting hormone-dependent ubiquitination and degradation of transcriptional repressor JASMONATE ZIM DOMAIN (JAZ) proteins. JAZ proteins are repressors of the jasmonic acid signaling pathway. COI1 proteins can form a co-receptor with one or more JAZ transcriptional repressor protein that can bind jasmonate. Formation, or lack of formation, of jasmonate/COI1/JAZ complexes can regulate the sophisticated, multilayered immune signaling network present in plants.

The stress hormone jasmonate (JA) plays a central role in regulating plant defenses against a variety of chewing insects and necrotrophic pathogens. Salicylic acid (SA) is another plant hormone that can be employed for plant defense against biotrophic or hemibiotrophic pathogens. During host-pathogen coevolution, however, many successful plant pathogens developed mechanisms to attack or hijack components of the plant immune signaling network as part of their pathogenesis strategies. As a result, the plant immune system, although powerful, is often fallible in the face of highly evolved pathogens.

Jasmonate is one of the common targets of virulence factors from highly evolved biotrophic/hemibiotrophic pathogens. Strains of the bacterial pathogen Pseudomonas syringae, for example, produce proteinaceous effectors, as well as a JA-mimicking toxin, coronatine (COR), to activate JA signaling and promote disease susceptibility. Higher plants synthesize different forms of JA, including the most bioactive form, jasmonoyl-L-isoleucine (JA-Ile). By way of example, structures of (3R,7S) JA-Ile and the JA-mimicking toxin, coronatine (COR), are shown below:

A plant's perception of JA-Ile (or COR) occurs through the COI1-JAZ co-receptor. Guided by the crystal structure of the JA receptor and evolutionary clues, the inventors have modified the JA receptor (COI1) to allow for sufficient endogenous JA signaling but greatly reduced sensitivity to COR. As illustrated herein, transgenic Arabidopsis expressing this modified COI1-containing receptor are not only fertile and maintain a high level of defense against insects, but also have the ability to resist COR-producing pathogens Pseudomonas syringae pv tomato and P. syringae pv maculicola.

In addition, the modified COI1 proteins do not form a complex with herbicide compounds as readily as do wild type, unmodified COI1 proteins. Accordingly, expression of the modified COI1 proteins described herein can confer herbicide resistance to plants. Hence, growth of weeds and undesired plants that do not express the modified COI1 proteins can be inhibited by application of herbicides, but plants that express the modified COI1 proteins described herein are resistant to the herbicides and grow well despite exposure to herbicides.

Ligands that Bind COI1

A variety of molecules can bind to COI1 protein. Jasmonic acid and variants thereof are the natural ligands of COI1. Higher plants synthesize different forms of jasmonic acid, including the most bioactive form jasmonoyl-L-isoleucine (JA-Ile). As described herein the modified COI1 polypeptides preferentially bind ligands such as jasmonic acid and JA-Ile, rather than a structurally related molecule, coronatine (COR), which is produced by several strains of Pseudomonas syringae. The differences in binding affinities between jasmonic acid variants and coronatine, mean that coronatine can be an effective herbicide for plants that do not express the modified COI1 polypeptides described herein. Only by expressing these modified COI1 proteins can plants grow well and resist infection by various pests when exposed to coronatine and other herbicides.

The types of molecules that can act as herbicides of plants that do not express the modified COI1 proteins include compounds of formula I:

wherein:

R₁ can be a three to six carbon (C₃ to C₆) alkyl that can have one double bond, or R₁ can be a C₃ to C₆ alkylene that can have one double bond and that links to R₂ to form a cycloalkyl ring;

R₂ can be a CH₂ or a CH;

A is a cyclopentyl ring;

B can be a C₃ to C₆ cycloalkyl ring or a heterocycloalkyl ring; and

R₃ can be a C₁ to C₃ alkyl; and

R₄ can be hydrogen or C₁ to C₃ alkyl.

The compounds of formula I bind with good affinity to wild type, unmodified COI1 proteins. Some researchers have reported that the highest biological activity in terms of JA-responses was observed with coronatine (COR) (Feys et al, Plant Cell 6: 751-59 (1994)). This high activity may be due in part to the (3R,7S)-configuration at the cyclopentanone ring of coronatine (COR). Structures for coronatine (COR) and different isomers of jasmonate-Ile are shown below.

In addition, various herbicides can bind to COI1 proteins, especially wild type COIL proteins. See Irvine et al. Pest Manag Sci 64: 891-899 (2008). For example, the structures of herbicides cinnacidin 1, and cinnacidin analogs 2 and 11 that can bind to COI1 proteins are shown below (id.).

COI1 Modifications

Plants, plant cells, and seeds described herein can express at least one type of modified COI1 protein. The modified COI1 proteins do not bind coronatine and herbicide ligands at the concentrations that wild type (or parental unmodified) COI1 proteins bind coronatine and herbicide ligands. Instead, much higher concentrations of coronatine and herbicide ligands are needed for formation of a complex with the modified COI1 proteins described herein. Hence, expression of the modified COI1 proteins in plants can protect the plants against bacterial infection and herbicides without compromising the plants' natural resistance to insects. Hence, at least 2-fold, at least 3-fold, at least 4-fold, at least 5-fold, at least 7-fold, at least 10-fold, at least 15-fold, at least 20-fold, at least 25-fold, at least 50-fold, at least 75-fold, at least 90-fold, at least 100-fold higher concentrations of coronatine and/or herbicide compounds are needed for formation of a complex with the modified COI1 proteins than are needed for formation of a complex with wild type or unmodified COI1 proteins.

The modified COI1 proteins can be expressed in plants, plant cells, and/or seeds from an expression cassette, transgene, or modified endogenous nucleic acid that encodes the modified COI1 protein.

Plants, plant cells, and seeds described herein can optionally have one or more genomic deletions, insertions, or substitutions in at least part of an endogenous COI1 gene. Such deletions, insertions, or substitutions can either alter the endogenous COI1 gene so that the endogenous gene encodes a modified COI1 protein, or the deletions, insertions, or substitutions can reduce/eliminate endogenous COI1 expression so that COI1 function can be replaced by a transgene encoding a modified COI1 protein. Rather than expression a native (e.g., endogenous, wild type) COI1 protein, the plants, plant cells, and seeds described herein can therefore express a modified COI1 protein. Expression of the modified COI1 protein can therefore be from a modified COI1 transgene, from a modified endogenous COI1 gene, or from a modified COI1 transgene that replaces an endogenous COI1 gene.

Deletions, insertions, or substitutions of endogenous COI1 genomic sequences can be generated site-specific recombination-mediated methods. Non-limiting examples of methods of introducing a modification into the genome of a plant cell can include microinjection, viral delivery, recombinase technologies, homologous recombination, TALENS, CRISPR, and/or ZFN, see, e.g. Clark and Whitelaw Nature Reviews Genetics 4:825-833 (2003); which is incorporated by reference herein in its entirety.

The mutations can range in size from one or two nucleotides to thousands of nucleotides (or any value therebetween). Deletions, insertions, and/or substitutions are created at a desired location in the genome. For example, borders (end points) of the deletions, insertions, or substitutions can be at defined locations to control the size of the deletions, insertions, or substitutions.

In some cases at least one amino acid is replaced with a hydrophobic amino acid. Examples of hydrophobic amino acids include valine, leucine, isoleucine, methionine, glycine, proline, or phenylalanine. In some cases the amino acid that is replaced can be an alanine. Hence, in many cases the amino acid that replaces the native, wild type, or parental COI1 protein is not an alanine. In other words, even though alanine may be a hydrophobic amino acid, in many cases no amino acid is replaced by alanine to generate a modified COI1 protein.

The mutation(s) can reduce or eliminate expression of endogenous COI1 genes within plant cells, plants, and seeds (e.g., so that a mutant COI1 transgene can provide expression of the modified COI1 protein). Alternatively, the mutations can modify the sequence of the endogenous COI1 gene(s) so that a modified COI1 protein is expressed.

For example, in some cases the mutations can eliminate transcription and/or translation of from an endogenous COI1 gene so that it can be replaced by a modified COI1 transgene. In some cases, the mutations can also eliminate transcription and/or translation of from genes related to a COI1 gene so that it can be replaced by a modified COI1 transgene.

For example, in some cases endogenous native (e.g., wild type) transcription and/or translation can be reduced by at least 40%, or at least 50%, or at least 60%, or at least 70%, or at least 80%, or at least 90%, or at least 95%, or at least 97%, or at least 99% compared to parental or wild type plant cells, plants, and seeds of the same species (that do not have the COI1 mutation(s)).

Mutation(s) that modify the sequence of a COI protein (expressed from a modified endogenous COI1 gene or from a transgene that encodes a modified COI1 protein) can reduce or eliminate interaction of the COI1 protein with one or more jasmonic acid-mimicking toxins. For example, the mutation(s) can reduce or eliminate COI1 protein interaction with a coronatine (COR), cinnacidin, or combinations thereof. For example, interaction between a COI1 protein and one or more jasmonic acid-mimicking toxins can be reduced by at least 40%, or at least 50%, or at least 60%, or at least 70%, or at least 80%, or at least 90%, or at least 95%, or at least 97%, or at least 99% compared to a native (e.g., unmodified, wild type) COI1 protein (that does not have the COI1 mutation(s)).

COI1 Sequences

As an example, an Arabidopsis thaliana COI1 protein with a sequence provided by the NCBI database as accession number O04197.1 (GI:59797640), is shown below as SEQ ID NO:1.

1 MEDPDIKRCK LSCVATVDDV IEQVMTYITD PKDRDSASLV 41 CRRWFKIDSE TREHVTMALC YTATPDRLSR RFPNLRSLKL 81 KGKP RA A MF N LIPENWGGYV TPWVTEISNN LRQLKSVHFR 121 RMIVSDLDLD RLAKARADDL ETLKLDKCSG FTTDGLLSIV 161 THCRKIKTLL MEESSFSEKD GKWLHELAQH NTSLEVLNFY 201 MTEFAKISPK DLETIARNCR SLVSVKVGDF EILELVGFFK 241 AAANLEEFCG GSLNEDIGMP EKYMNLVFPR KLCRLGLSYM 281 GPNEMPILFP FAAQIRKLDL LYALLETEDH CTLIQKCPNL 321 EVLETRNVIG DRGLEVLAQY CKOLKRLRIE RGAD E QGMED 361 EEGLVSQRGL IALAQGCQEL EYM A V Y VSDI TNESLESIGT 401 YLKNLCDF R L VLLDREERIT DLPLDNGVRS LLIGCKKLR R 441 FAF YLR QGGL TDLGLSYIGQ YSPNVR W M L L GYVGESDEGL 481 MEFSRGCPNL QKLEM R GCCF SERAIAAAVT KLPSLRYLWV 521 QGYRASMTGQ DLMQMARPYW NIELIPSRRV PEVNQQGEIR 561 EMEHPAHILA YYSLAGQRTD CPTTVRVLKE PI

The jasmonate binding pocket can include amino acids within about three amino acid positions of positions 85, 86, 88, 89, 355, 386, 409, 440, 444, 445, 446, 467, 469, and 496 (e.g., identified in bold and with underlining in the SEQ ID NO:1 sequence shown above). For example, in the Arabidopsis thaliana COI1 protein shown as SEQ ID NO:1 above, the jasmonate binding pocket can include amino acids within about three positions of R85, A86, M88, F89, E355, Y386, R409, R440, Y444, L445, R446, W467, L469, and R496.

In some embodiments, the modified COI1 protein have an amino acid substitution, replacement, deletion, or insertion at an amino acid position that directly contacts the jasmonate or coronatine ligand (e.g., a modification of any of positions 85, 86, 88, 89, 355, 386, 409, 440, 444, 445, 446, 467, 469, and 496 in the SEQ ID NO:1 sequence). However, in other embodiments, the modified COI1 protein have an amino acid substitution, replacement, deletion, or insertion at an amino acid position that does not directly contacts the ligand (e.g., a modification that is not at any of positions 85, 86, 88, 89, 355, 386, 409, 440, 444, 445, 446, 467, 469, and 496 in the SEQ ID NO:1 sequence).

For example, as described in more detail in the Examples, an alanine at position 384 of a COI1 protein was replaced with a valine to generate a modified COI1 protein with reduced COR binding and enhanced resistance to bacterial infection, but plants that express such a modified COI1 protein are fertile and normal levels of insect defense. A sequence for the modified Arabidopsis thaliana COI1 protein with valine at position 384 is shown below as SEQ ID NO:2.

1 MEDPDIKRCK LSCVATVDDV IEQVMTYITD PKDRDSASLV 41 CRRWFKIDSE TREHVTMALC YTATPDRLSR RFPNLRSLKL 81 KGKPRAAMFN LIPENWGGYV TPWVTEISNN LRQLKSVHFR 121 RMIVSDLDLD RLAKARADDL ETLKLDKCSG FTTDGLLSIV 161 THCRKIKTLL MEESSFSEKD GKWLHELAQH NTSLEVLNFY 201 MTEFAKISPK DLETIARNCR SLVSVKVGDF EILELVGFFK 241 AAANLEEFCG GSLNEDIGMP EKYMNLVFPR KLCRLGLSYM 281 GPNEMPILFP FAAQIRKLDL LYALLETEDH CTLIQKCPNL 321 EVLETRNVIG DRGLEVLAQY CKQLKRLRIE RGADEQGMED 361 EEGLVSQRGL IALAQGCQEL EYM V VYVSDI TNESLESIGT 401 YLKNLCDFRL VLLDREERIT DLPLDNGVRS LLIGCKKLRR 441 FAFYLRQGGL TDLGLSYIGO YSPNVRWMLL GYVGESDEGL 481 MEFSRGCPNL QKLEMRGCCF SERAIAAAVT KLPSLRYLWV 521 QGYRASMTGQ DLMQMARPYW NIELIPSRRV PEVNQQGEIR 561 EMEHPAHILA YYSLAGQRTD CPTTVRVLKE PI

An example of a nucleotide (cDNA) sequence that encodes the SEQ ID NO:1 COI1 protein (NCBI accession number NM_129552.4 (GI:1063702813)) is shown below as SEQ ID NO:3.

1 GCAAAAATGA AAAGAAAAAC ATAGAAGTAG AGAGAAGATC 41 GCATCTCGAC CGTCAACTTC AGTGTATGAA ATAATGATCG 81 TCCCACTTGA TCCTCAAAAA TATTATTAAC CAAACAAAAT 121 TTGATTCCAT CGTCCCACTT TCTTCTTCTT CCTCCCAATC 161 CGCCTCTTCT TCCTACGCGT GTCTTCTTCT CCCTCACTCT 201 CTCAATCTCT AGTCTTCTCC GATTCACCGG ATCTTTCCTT 241 TCTTACTTCT TTCTTCTCAC TCTGGTGGTT ATGTGTGGAT 281 CTGCGACCTC GATTTCAATT CGAAGTCGTC GGTTTCTTCT 321 CTAAATCGAA TCTTTCCAGG ATTCGTTTGT TTTTTTCTTT 361 TGTTTTTTTT TCGATCCGAT GGAGGATCCT GATATCAAGA 401 GGTGTAAATT GAGCTGCGTC GCGACGGTTG ATGATGTCAT 441 CGAGCAAGTC ATGACCTATA TAACTGACCC GAAAGATCGC 481 GATTCGGCTT CTTTGGTGTG TCGGAGATGG TTCAAGATTG 521 ATTCCGAGAC GAGAGAGCAT GTGACTATGG CGCTTTGCTA 561 CACTGCGACG CCTGATCGTC TTAGCCGTCG ATTCCCGAAC 601 TTGAGGTCGC TCAAGCTTAA AGGCAAGCCT AGAGCAGCTA 641 TGTTTAATCT GATCCCTGAG AACTGGGGAG GTTATGTTAC 681 TCCTTGGGTT ACTGAGATTT CTAACAACCT TAGGCAGCTC 721 AAATCGGTGC ACTTCCGACG GATGATTGTC AGTGACTTAG 761 ATCTAGATCG TTTAGCTAAA GCTAGAGCAG ATGATCTTGA 801 GACTTTGAAG CTAGACAAGT GTTCTGGTTT TACTACTGAT 841 GGACTTTTGA GCATCGTTAC ACACTGCAGG AAAATAAAAA 881 CTTTGTTAAT GGAAGAGAGT TCTTTTAGTG AAAAGGATGG 921 TAAGTGGCTT CATGAGCTTG CTCAGCACAA CACATCTCTT 961 GAGGTTTTAA ACTTCTACAT GACGGAGTTT GCCAAAATCA 1001 GTCCCAAAGA CTTGGAAACC ATAGCTAGAA ATTGCCGCTC 1041 TCTGGTATCT GTGAAGGTCG GTGACTTTGA GATTTTGGAA 1081 CTAGTTGGGT TCTTTAAGGC TGCAGCTAAT CTTGAAGAAT 1121 TTTGTGGTGG CTCCTTGAAT GAGGATATTG GAATGCCTGA 1161 GAAGTACATG AATCTGGTTT TTCCCCGAAA ACTATGTCGG 1201 CTTGGTCTCT CTTACATGGG ACCTAATGAA ATGCCAATAC 1241 TATTTCCATT CGCGGCCCAA ATCCGAAAGC TGGATTTGCT 1281 TTATGCATTG CTAGAAACTG AAGACCATTG TACGCTTATC 1321 CAAAAGTGTC CTAATTTGGA AGTTCTCGAG ACAAGGAATG 1361 TAATCGGAGA TAGGGGTCTA GAGGTCCTTG CACAGTACTG 1401 TAAGCAGTTG AAGCGGCTGA GGATTGAACG CGGTGCAGAT 1441 GAACAAGGAA TGGAGGACGA AGAAGGCTTA GTCTCACAAA 1481 GAGGATTAAT CGCTTTGGCT CAGGGCTGCC AGGAGCTAGA 1521 ATACATGGCG GTGTATGTCT CAGATATAAC TAACGAATCT 1561 CTTGAAAGCA TAGGCACATA TCTGAAAAAC CTCTGTGACT 1601 TCCGCCTTGT CTTACTCGAC CGGGAAGAAA GGATTACAGA 1641 TCTGCCACTG GACAACGGAG TCCGATCTCT TTTGATTGGA 1681 TGCAAGAAAC TCAGACGATT TGCATTCTAT CTGAGACAAG 1721 GCGGCTTAAC CGACTTGGGC TTAAGCTACA TCGGACAGTA 1761 CAGTCCAAAC GTGAGATGGA TGCTGCTGGG TTACGTAGGT 1801 GAATCAGATG AAGGTTTAAT GGAATTCTCA AGAGGCTGTC 1841 CAAATCTACA GAAGCTAGAG ATGAGAGGTT GTTGCTTCAG 1881 TGAGCGAGCA ATCGCTGCAG CGGTTACAAA ATTGCCTTCA 1921 CTGAGATACT TGTGGGTACA AGGTTACAGA GCATCGATGA 1961 CGGGACAAGA TCTAATGCAG ATGGCTAGAC CGTACTGGAA 2001 CATCGAGCTG ATTCCATCAA GAAGAGTCCC GGAAGTGAAT 2041 CAACAAGGAG AGATAAGAGA GATGGAGCAT CCGGCTCATA 2081 TATTGGCTTA CTACTCTCTG GCTGGCCAGA GAACAGATTG 2121 TCCAACAACT GTTAGAGTCC TGAAGGAGCC AATATGATAT 2161 GACCCAAAAA ACAGGTTTGT ATATAAAGAT TTTTAGTCTC 2201 GAGTTTTGGG GTTTCCACAA ACTGTGTACT ATACTACTTT 2241 GGTTCTTTTT TTGTTTCATG TTGTGTCGTC GATGTTTTTG 2281 GGAGATTACA TAGAGTCAGT CTTGTTTGTT GTATGGTCAT 2321 TACTTCTTTA TTTTTCCTCA GGGGTCTGTT TACTTTAATT 2361 TCTTTAATAA AACCCCGAAG ATTTTGAGAG ATTTCTTTAT 2401 CGTCCATGGT GTTGACTTCT GAGAGCTATA TTTGTTTGGA 2441 TTGGCATCTG AAACTTTATT TGTGGTTGTG ATTGTTTTGA 2481 TAACATTAGT AAAAAGGCAA ATAATAGAGT AC

An example of a COI1 protein from Brassica rapa (turnip) with NCBI accession number XP_009133392.1 (GI:685284974) has the following sequence (SEQ ID NO:4).

1 MEDPDIKKCR LSSVTVDDVI EQVMPYITDP KDRDSASLVC 41 RRWFEIDSET REHVTMALCY TSTPDRLSRR FPNLRSIKLK 81 GKPRAAMFNL IPENWGGFVT PWVNEIASSL RRLKSVHFRR 121 MIVSDLDLDV LAKARLDELE ALKLDKCSGF STDGLFSIVK 161 HCRKMKTLLM EESSFVEKDG NWLHELALHN TSLEVLNFYM 201 TEFAKINAKD LESIARNCRS LVSVKIGDFE MLELVGFFKA 241 ATNLEEFCGG SLNEEIGRPE KYMNLTFPPK LCCLGLSYMG 281 PNEMPILFPF AAQIRKLDLI YALLATEDHC TLIQKCPNLE 321 VLETRNVIGD RGLEVLGQCC KKLKRLRIER GEDEQGMEDE 361 EGLVSQRGLV ALAQGCQELE YM A VYVSDIT NESLESIGTY 401 LKNLCDFRLV LLDQEERITD LPLDNGVRSL LIGCKKLRRF 441 AFYLRQGGLT DVGLSYIGQY SPNVRWMLLG YVGESDEGLM 481 EFSRGCPKLQ KLEMRGCCFS ERAIAAAVLK IPSLRYLWVQ 521 GYRASTTGQD LRLMSRPYWN IELIPARKVP EVNQLGEVRE 561 MEHPAHILAY YSLAGERTDC PPTVKVLREA

A comparison of the Arabidopsis thaliana COI1 SEQ ID NO:1 sequence and the Brassica rapa COI SEQ ID NO:4 sequence is shown below, illustrating that the two proteins have at least 90% sequence identity. In addition, the location of the alanine at position 384 that can be replaced, for example with a valine, to generate a modified COI1 protein is also identified in bold and with underlining. As illustrated, this alanine is at about position 383 in the Brassica rapa COI1 SEQ ID NO:4 sequence.

89.8% identity in 590 residues overlap; Score: 2792.0; Gap frequency: 0.2% Seq1 1 MEDPDIKRCKLSCVATVDDVIEQVMTYITDPKDRDSASLVCRRWFKIDSETREHVTMALC Seq4 1 MEDPDIKKCRLSSV-TVDDVIEQVMPYITDPKDRDSASLVCRRWFEIDSETREHVTMALC ******* * ** * ********** ******************* ************** Seq1 61 YTATPDRLSRRFPNLRSLKLKGKPRAAMFNLIPENWGGYVTPWVTEISNNLRQLKSVHFR Seq4 60 YTSTPDRLSRRFPNLRSIKLKGKPRAAMFNLIPENWGGFVTPWVNEIASSLRRLKSVHFR ** ************** ******************** ***** **   ** ******* Seq1 121 RMIVSDLDLDRLAKARADDLETLKLDKCSGFTTDGLLSIVTHCRKIKTLLMEESSFSEKD Seq4 120 RMIVSDLDLDVLAKARLDELEALKLDKCSGFSTDGLFSIVKHCRKMKTLLMEESSFVEKD ********** ***** * ** ********* **** *** **** ********** *** Seq1 181 GKWLHELAQHNTSLEVLNKYMTEFAKISPKDLETIARNCRSLVSVKVGDFEILELVGFFK Seq4 180 GNWLHELALHNTSLEVLNFYMTEFAKINAKDLESIARNCRSLVSVKIGDFEMLELVGFFK * ****** ******************  **** ************ **** ******** Seq1 241 AAANLEEFCGGSLNEDIGMPEKYMNLVFPRKLCRLGLSYMGPNEMPILFPFAAQIRKLDL Seq4 240 AATNLEEFCGGSLNEEIGRPEKYMNLIFPPKLCCLGLSYMGPNEMPILFPFAAQIRKLDL ** ************ ** ******* ** *** ************************** Seq1 301 LYALLETEDHCTLIQKCPNLEVLETRNVIGDRGLEVLAQYCKQLKRLRIERGADEQGMED Seq4 300 IYALLATEDHCTLIQKCPNLEVLETRNVIGDRGLEVLGQCCKKLKRLRIERGEDEQGMED  **** ******************************* * ** ********* ******* Seq1 361 EEGLVSQRGLIALAQGCQELEYM A VYVSDITNESLESIGTYLKNLCDFRLVLLDREERIT Seq4 360 EEGLVSQRGLVALAQGCQELEYM A VYVSDITNESLESIGTYLKNLCDFRLVLLDQEERIT ********** ******************************************* ***** Seq1 421 DLPLDNGVRSLLIGCKKLRRFAFYLRQGGLTDLGLSYIGQYSPNVRWMLLGYVGESDEGL Seq4 420 DLPLDNGVRSLLIGCKKLRRFAFYLRQGGLTDVGLSYIGQYSPNVRWMLLGYVGESDEGL ******************************** *************************** Seq1 481 MEFSRGCPNLQKLEMRGCCFSERAIAAAVTKLPSLRYLWVQGYRASMTGQLMQMARPYW Seq4 480 MEFSRGCPKLQKLEMRGCCFSERAIAAAVLKIPSLRYLWVQGYRASTTGQDLRLMSRPYW ******** ******************** * ************** *****  * **** Seq1 541 NIELIPSRRVPEVNQQGEIREMEHPAHILAYYSLAGQRTDCPTTVRVLKE Seq4 540 NIELIPARKVPEVNQLGEVREMEHPAHILAYYSLAGERTDCPPTVKVLRE ****** * ****** ** ***************** ***** ** ** * An example of a modified COI1 protein from Brassica rapa (turnip) with a valine instead of the alanine at position 383 (as shown in SEQ ID NO:4) can have the following sequence (SEQ ID NO:5).

1 MEDPDIKKCR LSSVTVDDVI EQVMPYITDP KDRDSASLVC 41 RRWFEIDSET REHVTMALCY TSTPDRLSRR FPNLRSIKLK 81 GKPRAAMFNL IPENWGGFVT PWVNEIASSL RRLKSVHFRR 121 MIVSDLDLDV LAKARLDELE ALKLDKCSGF STDGLFSIVK 161 HCRKMKTLLM EESSFVEKDG NWLHELALHN TSLEVLNFYM 201 TEFAKINAKD LESIARNCRS LVSVKIGDFE MLELVGFFKA 241 ATNLEEFCGG SLNEEIGRPE KYMNLTFPPK LCCLGLSYMG 281 PNEMPILFPF AAQIRKLDLI YALLATEDHC TLIQKCPNLE 321 VLETRNVIGD RGLEVLGQCC KKLKRLRIER GEDEQGMEDE 361 EGLVSQRGLV ALAQGCQELE YM V VYVSDIT NESLESIGTY 401 LKNLCDFRLV LLDQEERITD LPLDNGVRSL LIGCKKLRRF 441 AFYLRQGGLT DVGLSYIGQY SPNVRWMLLG YVGESDEGLM 481 EFSRGCPKLQ KLEMRGCCFS ERAIAAAVLK IPSLRYLWVQ 521 GYRASTTGQD LRLMSRPYWN IELIPARKVP EVNQLGEVRE 561 MEHPAHILAY YSLAGERTDC PPTVKVLREA

An example of a nucleotide (cDNA) sequence that encodes the SEQ ID NO:4 Brassica rapa (turnip) COI protein (NCBI cDNA accession number XM_009135144.1 (GI:685284973)) is shown below as SEQ ID NO:6.

1 GCCACTTCTT CCTCCTCTCC TCACGCTCCA CGTCCCCTGC 41 TAGCATCCCT CCCGCTTCCT CCTCCGATCT CTGCTCGTCT 81 TATCTTCACT CTCTACTGTA TTACTTTGGA TCTGCGAGAG 121 ATTCGTGTAA TTGAAATCGA TCTCGTCCCT CAGCTGGTAT 161 TCGAATTTGT TGATTGTTTT GGTTTGTTTT AGATTCGATT 201 TCGATTTGTT ACATGGAGGA TCCGGATATC AAGAAGTGCA 241 GATTGAGCTC CGTGACGGTC GATGACGTCA TCGAGCAGGT 281 CATGCCTTAC ATAACCGATC CGAAAGATCG AGACTCCGCT 321 TCCCTCGTGT GCCGGAGGTG GTTCGAGATC GACTCCGAGA 361 CGAGGGAGCA CGTGACCATG GCCTTGTGCT ACACCTCGAC 401 GCCCGATCGT CTCAGCCGTA GGTTTCCCAA TCTGAGGTCG 441 ATCAAGCTCA AAGGGAAGCC GAGAGCAGCT ATGTTCAATC 481 TCATCCCCGA GAACTGGGGA GGGTTTGTTA CCCCTTGGGT 521 CAACGAGATA GCTTCGTCGC TGCGAAGGCT CAAGTCTGTG 561 CATTTTAGGC GGATGATTGT GAGCGATTTG GATCTGGATG 601 TTTTGGCTAA GGCGAGGTTG GATGAGCTCG AGGCGTTGAA 641 GCTTGATAAG TGCTCGGGTT TCTCTACGGA TGGACTTTTC 681 AGCATCGTTA AGCACTGCAG GAAAATGAAA ACATTGTTAA 721 TGGAAGAGAG TTCTTTTGTT GAAAAGGATG GTAACTGGCT 761 TCATGAACTT GCTCTGCACA ACACTTCTCT CGAGGTTCTA 801 AATTTCTACA TGACTGAGTT TGCAAAAATC AATGCCAAAG 841 ACTTGGAAAG CATAGCTAGA AATTGCCGCT CTCTGGTTTC 881 TGTGAAGATC GGTGACTTTG AGATGTTGGA ACTAGTCGGG 921 TTCTTTAAAG CTGCAACTAA TCTTGAAGAA TTTTGTGGTG 961 GCTCCTTAAA TGAAGAAATT GGAAGACCGG AGAAGTATAT 1001 GAATCTGACT TTCCCTCCAA AACTATGTTG TCTGGGCCTT 1041 TCTTACATGG GACCTAATGA AATGCCAATA CTGTTTCCAT 1081 TCGCTGCCCA AATCCGGAAG CTGGATCTGA TCTATGCATT 1121 GCTCGCAACT GAGGATCATT GTACACTTAT TCAAAAGTGT 1161 CCTAATTTGG AAGTTCTCGA GACAAGGAAT GTAATTGGAG 1201 ATAGGGGTCT AGAGGTTCTT GGACAGTGCT GTAAGAAGTT 1241 GAAGCGGCTG AGGATTGAAC GGGGTGAAGA TGAACAAGGA 1281 ATGGAGGATG AAGAAGGCTT AGTCTCACAA AGAGGATTAG 1321 TCGCTTTGGC TCAGGGCTGC CAGGAGCTAG AATACATGGC 1361 GGTGTATGTC TCAGATATAA CCAACGAGTC TCTCGAAAGC 1401 ATAGGCACAT ATCTGAAAAA CCTCTGTGAC TTCCGCCTCG 1441 TCTTACTCGA CCAAGAAGAG AGAATAACAG ATCTGCCACT 1481 GGACAACGGA GTCAGATCCC TCTTGATCGG ATGCAAAAAA 1521 CTCAGACGGT TTGCATTCTA TCTCAGACAA GGCGGCTTAA 1561 CAGACGTGGG GTTAAGCTAC ATCGGACAGT ACAGTCCAAA 1601 CGTGAGGTGG ATGCTTCTCG GTTACGTTGG TGAATCAGAC 1641 GAAGGCCTAA TGGAATTCTC AAGAGGATGT CCGAAACTAC 1681 AGAAGCTGGA GATGAGAGGT TGTTGCTTCA GCGAGCGAGC 1721 AATAGCTGCA GCGGTACTGA AAATCCCTTC GCTGAGATAC 1761 CTGTGGGTAC AAGGCTATAG AGCATCGACG ACGGGACAAG 1801 ACCTGAGGCT AATGTCTAGA CCGTACTGGA ACATCGAGCT 1841 GATTCCGGCA AGAAAAGTCC CGGAAGTGAA TCAGCTTGGA 1881 GAGGTGAGAG AGATGGAGCA TCCTGCTCAT ATACTGGCTT 1921 ACTACTCTCT GGCTGGTGAG AGAACAGATT GTCCACCAAC 1961 GGTTAAAGTC CTGAGGGAGG CATGATGATG ATGATGAAAA 2001 GCAGGTTTGT ACATAAAGAT TTGGTTTTGA GGTTTCCACG 2041 AACTGTCGAA TGGATTCTAT TTTTTCTTTA TTGGTGTATT 2081 GTCTGTAGTT TTGAGAGATT CCATAAAGAC TTTTGAGAGA 2121 TTGAAATAAG AAGAGAGAAA ACTAGTCTTT CAGAAGA

An example of a COI1 protein from Brassica napus (rapeseed) with NCBI accession number CDY60996.1 (GI:674872982) has the following sequence (SEQ ID NO:7).

1 MLQRIFWMFF FSFNMLTRYF IKTPPGYFCR LARCAAYATR 41 LTKQTDSIAS SPPSIYIKNN NYPLCPLDPK LLLLLSTLLI 81 PSFTHTYATS SSSPHAPQIR VIEIDLIRFR FVTMEDPDIK 121 KCRLSSVTVD DVIEQVMPYI TDPKDRDSAS LVCRRWFEID 161 SETREHVTMA LCYTSTPDRL SRRFPNLRSI KLKGKPRAAM 201 FNLIPENWGG FVTPWVNEIA SSLRRLKSVH FRRMIVSDLD 241 LDVLAKARLD ELEALKLDKC SGFSTDGLFS IVKHCRKMKT 281 LLMEESSFVE KDGNWLHELA LHNTSLEVLN FYMTEFAKIN 321 AKDLESIARN CRSLVSVKIG DFEMLELVGF FKAATNLEEF 361 CGGSLNEEIG RPEKYMNLTF PPKLCCLGLS YMGPNEMPIL 401 FPFAAQIRKL DLIYALLATE DHCTLIQKCP NLEVLETRNV 441 IGDRGLEVLG QCCKKLKRLR IERGEDEQGM EDEEGLVSQR 481 GLVALAQGCQ ELEYM A VYVS DITNESLESI GTYLKNLCDF 521 RLVLLDQEER ITDLPLDNGV RSLLIGCKKL RRFAFYLRQS 561 GLTDVGLSYI GQYSPNVRWM LLGYVGESDE GLMEFSRGCP 601 KLQKLEMRGC CFSERAIAAA VLKIPSLRYL WVQGYRASTT 641 GQDLRLMSRP YWNIELIPAR KVPEVNQLGE VREMEHPAHI 681 LAYYSLAGER TDCPPTVKVL REA

A comparison of the Arabidopsis thaliana COI1 SEQ ID NO:1 sequence and the Brassica napus COI SEQ ID NO:7 sequence is shown below, illustrating that the two proteins have at least 90% sequence identity. In addition, the location of the alanine at position 384 (of SEQ ID NO:1) that can be replaced, for example with a valine, to generate a modified COI1 protein is also identified in bold and with underlining. As illustrated, this alanine is at about position 496 in the Brassica napus COI1 SEQ ID NO:7 sequence.

89.7% identity in 590 residues overlap; Score: 2786.0; Gap frequency: 0.2% Seq1 1 MEDPDIKRCKLSCVATVDDVIEQVMTYITDPKDRDSASLVCRRWFKIDSETREHVTMALC Seq7 114 MEDPDIKKCRLSSV-TVDDVIEQVMPYITDPKDRDSASLVCRRWFEIDSETREHVTMALC ******* * ** * ********** ******************* ************** Seq1 61 YTATPDRLSRRFPNLRSLKLKGKPRAAMFNLIPENWGGYVTPWVTEISNNLRQLKSVHFR Seq7 173 YTSTPDRLSRRFPNLRSIKLKGKPRAAMFNLIPENWGGFVTPWVNEIASSLRRLKSVHFR ** ************** ******************** ***** **   ** ******* Seq1 121 RMIVSDLDLDRLAKARADDLETLKLDKCSGFTTDGLLSIVTHCRKIKTLLMEESSFSEKD Seq7 233 RMIVSDLDLDVLAKARLDELEALKLDKCSGFSTDGLFSIVKHCRKMKTLLMEESSFVEKD ********** ***** * ** ********* **** *** **** ********** *** Seq1 181 GKWLHELAQHNTSLEVLNFYMTEFAKISPKDLETIARNCRSLVSVKVGDFEILELVGFFK Seq7 293 GNWLHELALHNTSLEVLNFYMTEFAKINAKDLESIARNCRSLVSVKIGDFEMLELVGFFK * ****** ******************  **** ************ **** ******** Seq1 241 AAANLEEFCGGSLNEDIGMPEKYMNLVFPRKLCRLGLSYMGPNEMPILFPFAAQIRKLDL Seq7 353 AATNLEEFCGGSLNEEIGRPEKYMNLTFPPKLCCLGLSYMGPNEMPILFPFAAQIRKLDL ** ************ ** ******* ** *** ************************** Seq1 301 LYALLETEDHCTLIQKCPNLEVLETRNVIGDRGLEVLAQYCKQLKRLRIERGADEQGMED Seq7 413 IYALLATEDHCTLIQKCPNLEVLETPNVIGDRGLEVLGQCCKKLKRLRIERGEDEQGMED  **** ******************************* * ** ********* ******* Seq1 361 EEGLVSQRGLIALAQGCQELEYM A VYVSDITNESLESIGTYLKNLCDFRLVLLDREERIT Seq7 473 EEGLVSQRGLVALAQGCQELEYM A VYVSDITNESLESIGTYIKNLCDFRLVLLDQEERIT ********** ******************************************* ***** Seq1 421 DLPLPLDNGVRSLLIGCKKLRRFAFYLRQGGLTDLGLSYIGQYSPNVRWMLLGYVGESDEGL Seq7 533 DLPLPLDNGVRSLLIGCKKLRRFAFYLRQSGLTDVGLSYIGQYSPNVRWMLLGYVGESDEGL *************************** **** *************************** Seq1 481 MEFSRGCPNLQKLEMRGCCFSERAIAAAVTKLPSLRYLWVQGYRASMTGQDLMQMARPYW Seq7 593 MEFSRGCPKLQKLEMRGCCFSERAIAAAVLKIPSLRYLWVQGYRASTTGQDLRLMSRPYW ******** ******************** * ************** *****  * **** Seq1 541 NIELIPSRRVPEVNQQGEIREMEHPAHILAYYSLAGQRTDCPTTVRVLKE Seq7 653 NIELIPARKVPEVNQLGEVREMEHPAHILAYYSLAGERTDCPPTVKVLRE ****** * ****** ** ***************** ***** ** ** *

An example of a modified COI1 Brassica napus (rapeseed) protein with a valine at position 496 instead of an alanine has the following sequence (SEQ ID NO:8).

1 MLQRIFWMFF FSFNMLTRYF IKTPPGYFCR LARCAAYATR 41 LTKQTDSIAS SPPSIYIKNN NYPLCPLDPK LLLLLSTLLI 81 PSFTHTYATS SSSPHAPQIR VIEIDLIRFR FVTMEDPDIK 121 KCRLSSVTVD DVIEQVMPYI TDPKDRDSAS LVCRRWFEID 161 SETREHVTMA LCYTSTPDRL SRRFPNLRSI KLKGKPRAAM 201 FNLIPENWGG FVTPWVNEIA SSLRRLKSVH FRRMIVSDLD 241 LDVLAKARLD ELEALKLDKC SGFSTDGLFS IVKHCRKMKT 281 LLMEESSFVE KDGNWLHELA LHNTSLEVLN FYMTEFAKIN 321 AKDLESIARN CRSLVSVKIG DFEMLELVGF FKAATNLEEF 361 CGGSLNEEIG RPEKYMNLTF PPKLCCLGLS YMGPNEMPIL 401 FPFAAQIRKL DLIYALLATE DHCTLIQKCP NLEVLETRNV 441 IGDRGLEVLG QCCKKLKRLR IERGEDEQGM EDEEGLVSQR 481 GLVALAQGCQ ELEYM V VYVS DITNESLESI GTYLKNLCDF 521 RLVLLDQEER ITDLPLDNGV RSLLIGCKKL RRFAFYLRQS 561 GLTDVGLSYI GQYSPNVRWM LLGYVGESDE GLMEFSRGCP 601 KLQKLEMRGC CFSERAIAAA VLKIPSLRYL WVQGYRASTT 641 GQDLRLMSRP YWNIELIPAR KVPEVNQLGE VREMEHPAHI 681 LAYYSLAGER TDCPPTVKVL REA

An example of a COI1 protein from Brassica oleracea (cabbage, Brussel sprouts, kale, cauliflower, etc.) with NCBI accession number XP_013628733.1 (GI:922451771) has the following sequence (SEQ ID NO:9).

1 MTMEDPDIKK CRLSSVTVDD VIEQVMPYIT DPKDRDSASL 41 VCRRWFEIDS ETREHVTMAL CYTSTPDRLS RRFPNLRSIK 81 LKGKPRAAMF NLIPENWGGF VTPWVNEVAS SLPRLKSVHF 121 RRMIVSDLDL DVLAKARLDE LEALKLDKCS GFSTDGLFSI 161 VKHCRKMKTL LMEESSFVEK DGNWLHELAL HNTSLEVLNF 201 YMTEFAKINA KDLESIARNC RSLVSVKIGD FEMLELVGFF 241 KAATNLEEFC GGSFNEEIGR PEKYMNLTFP PKLCCLGLSY 281 MGPNEMPILF PFAAQIRKLD LIYALLATED HCTLIQKCPN 321 LEVLETRNVI GDRGLEVLGQ CCKKLKRLRI ERGEDEQGME 361 DEEGLVSQRG LVALAQGCQE LEYM A VYVSD ITNESLESIG 401 TYLKNLCDFR LVLLDQEERI TDLPLDNGVR SLLIGCKKLR 441 RFAFYLRQGG LTDVGLSYIG QYSPNVRWML LGYVGESDEG 481 LMEFSRGCPK LQKLEMRGCC FSERAIAAAV LKIPSLRYLW 521 VQGYRASTTG QDLRLMSRPY WNIELIPARK VPEVNQLGEV 561 REMEHPAHIL AYYSLAGERT DCPPTVKVLR EA

A comparison of the Arabidopsis thaliana COI1 SEQ ID NO:1 sequence and the Brassica oleracea COI1 SEQ ID NO:9 sequence is shown below, illustrating that the two proteins have at least 89% sequence identity. In addition, the location of the alanine at position 384 that can be replaced, for example with a valine, to generate a modified COI1 protein is also identified in bold and with underlining. As illustrated, this alanine is at about position 385 in the Brassica oleracea COI1 SEQ ID NO:9 sequence.

89.3% identity in 590 residues overlap; Score: 2780.0; Gap frequency: 0.2% Seq1 1 MEDPDIKRCKLSCVATVDDVIEQVMTYITDPKDRDSASLVCRRWFKIDSETREHVTMALC Seq9 3 MEDPDIKKCRLSSV-TVDDVIEQVMPYITDPKDRDSASLVCRRWFEIDSETREHVTMALC ******* * ** * ********** ******************* ************** Seq1 61 YTATPDRLSRRFPNLRSLKLKGKPRAAMFNLIPENWGGYVTPWVTEISNNLRQLKSVHFR Seq9 62 YTSTPDRLSRRFPNLRSIKLKGKPRAAMFNLIPENWGGEVTPWVNEVASSLPRLKSVHFR ** ************** ******************** ***** *    *  ******* Seq1 121 RMIVSDLDLDRLAKARADDLETLKLDKCSGFTTDGLLSIVTHCRKIKTLLMEESSFSEKD Seq9 122 RMIVSDLDLDVLAKARLDELEALKLDKCSGFSTDGLFSIVKHCRKMKTLLMEESSFVEKD ********** ***** * ** ********* **** *** **** ********** *** Seq1 181 GKWLHELAQHNTSLEVLNFYMTEFAKISPKDLETIAPNCRSLVSVKVGDFEILELVGFFK Seq9 182 GNWLHELALHNTSLEVLNFYMTEFAKINAKDLESIARNCRSLVEVKIGDFEMLELVGFFK * ****** ******************  **** ************ **** ******** Seq1 241 AAANLEEFCGGSLNEDIGMPEKYMNLVFPRKLCRLGLSYMGPNEMPILFPFAAQIRYLDL Seq9 242 AATNLEEFCGGSFNEEIGRPEKYMNLTFPPKLCCLGLSYMGPNEMPILFPFAAQIRKLDL ** ********* ** ** ******* ** *** ************************** Seq1 301 LYALLETEDHCTLIQKCPNLEVLETRNVIGDRGLEVLACYCKQLKRLRIERGADEQGMED Seq9 302 IYALLATEDHCTLIQKCPNLEVLETRNVIGDRGLEVLGQCCKKLKRLRIERGEDEQGMED  **** ******************************* * ** ********* ******* Seq1 361 EEGLVSQRGLIALAQGCQELEYM A VYVSDITNESLESIGTYLKNLCDFRLVLLDREERIT Seq9 362 EEGLVSQRGLVALAQGCQELEYM A VYVSDITNESLESIGTYLKNLCDFRLVLLDQEERIT ********** ******************************************* ***** Seq1 421 DLPLDNGVRSLLIGCKKLRRFAFYLRQGGLTDLGLSYIGQYSPNVRWMLLGYVGESDEGL Seq9 422 DLPLDNGVRSLLIGCKKLRRFAFYLRQGGLTDVGLSYIGQYSPNVRWMLLGYVGESDEGL ******************************** *************************** Seq1 481 MEFSRGCPNLQKLEMRGCCFSERAIAAAVTKLPSLRYLWVQGYRASMTGQDLMQMARPYW Seq9 482 MEFSRGCPKLQKLEMRGCCFSERAIAAAVLKIPSLRYLWVQGYRASTTGQDLRLMSRPYW ******** ******************** * ************** ***** * **** Seq1 541 NIELIPSRRVPEVNQQEIREMEHPAHILAYYSLAGQRTDCPTTVRVLKE Seq9 542 NIELIPARKVPEVNQLGEVREMEHPAHILAYYSLAGERTDCPPTVKVLRE ****** * ****** ** ***************** ***** ** ** *

An example of a modified Brassica oleracea COI1 protein with a valine instead of an alanine at position 385 has the following sequence (SEQ ID NO:10).

1 MTMEDPDIKK CRLSSVTVDD VIEQVMPYIT DPKDRDSASL 41 VCRRWFEIDS ETREHVTMAL CYTSTPDRLS RRFPNLRSIK 81 LKGKPRAAMF NLIPENWGGF VTPWVNEVAS SLPRLKSVHF 121 RRMIVSDLDL DVLAKARLDE LEALKLDKCS GFSTDGLFSI 161 VKHCRKMKTL LMEESSFVEK DGNWLHELAL HNTSLEVLNF 201 YMTEFAKINA KDLESIARNC RSLVSVKIGD FEMLELVGFF 241 KAATNLEEFC GGSFNEEIGR PEKYMNLTFP PKLCCLGLSY 281 MGPNEMPILF PFAAQIRKLD LIYALLATED HCTLIQKCPN 321 LEVLETRNVI GDRGLEVLGQ CCKKLKRLRI ERGEDEQGME 361 DEEGLVSQRG LVALAQGCQE LEYM V VYVSD ITNESLESIG 401 TYLKNLCDFR LVLLDQEERI TDLPLDNGVR SLLIGCKKLR 441 RFAFYLRQGG LTDVGLSYIG QYSPNVRWML LGYVGESDEG 481 LMEFSRGCPK LQKLEMRGCC FSERAIAAAV LKIPSLRYLW 521 VQGYRASTTG QDLRLMSRPY WNIELIPARK VPEVNQLGEV 561 REMEHPAHIL AYYSLAGERT DCPPTVKVLR EA

An example of a nucleotide (cDNA) sequence that encodes the Brassica oleracea SEQ ID NO:9 COI1 protein (NCBI cDNA accession number XM_013773279.1 (GI:922451770)) is shown below as SEQ ID NO:11.

1 ATTATTATTA TCAACACTTT TGATTCCTTC CTCCACACAC 41 ACTCACGCCA CTTCTTCCTC CTCTCCTCAC GCTCCACCTA 81 TCGTGATTCC TATACTCGAT TTCGATTTGT TATCCGTTTG 121 TTTGATGACG ATGGAGGATC CGGATATCAA GAAGTGCAGA 161 TTGAGCTCCG TGACGGTCGA TGACGTCATC GAGCAGGTCA 201 TGCCTTACAT AACCGATCCG AAAGATCGAG ACTCCGCTTC 241 CCTCGTGTGC CGGAGGTGGT TCGAGATCGA CTCCGAGACG 281 AGGGAGCACG TGACCATGGC ACTATGCTAC ACCTCGACTC 321 CTGACCGTCT CAGCCGTAGG TTTCCGAATC TGAGGTCGAT 361 TAAGCTCAAA GGGAAGCCGA GAGCAGCTAT GTTCAATCTC 401 ATCCCCGAGA ACTGGGGAGG GTTTGTTACC CCTTGGGTCA 441 ACGAGGTAGC TTCATCTCTG CCAAGGCTCA AGTCTGTGCA 481 TTTTAGGCGG ATGATTGTCA GCGATTTGGA TCTTGATGTT 521 TTGGCTAAGG CGAGGTTGGA TGAGCTCGAG GCGTTGAAGC 561 TCGATAAGTG CTCAGGTTTC TCTACGGATG GACTTTTCAG 601 CATCGTTAAG CACTGCAGGA AAATGAAAAC ATTGTTAATG 641 GAAGAGAGTT CTTTTGTTGA AAAGGATGGT AACTGGCTGC 681 ATGAACTTGC TCTGCACAAC ACTTCTCTTG AGGTTCTAAA 721 TTTCTACATG ACTGAGTTTG CAAAAATCAA TGCCAAAGAC 761 TTGGAAAGCA TAGCTAGAAA TTGCCGCTCT CTGGTTTCTG 801 TGAAGATCGG TGACTTTGAG ATGTTGGAAC TAGTCGGGTT 841 CTTTAAAGCT GCAACTAATC TTGAAGAATT TTGTGGCGGC 881 TCCTTCAATG AAGAAATTGG AAGACCGGAG AAGTATATGA 921 ATCTGACTTT CCCTCCAAAA CTATGTTGTC TTGGCCTTTC 961 TTACATGGGA CCTAATGAAA TGCCAATACT GTTTCCATTC 1001 GCTGCCCAAA TCCGGAAGCT GGATCTGATC TATGCATTGC 1041 TCGCAACTGA GGATCATTGT ACACTTATTC AAAAGTGTCC 1081 TAATTTGGAA GTTCTCGAGA CAAGGAATGT AATTGGAGAT 1121 AGGGGTCTAG AGGTTCTTGG ACAGTGCTGT AAGAAGTTGA 1161 AGCGGCTGAG GATTGAACGG GGTGAAGATG AACAAGGAAT 1201 GGAGGATGAA GAAGGCCTAG TATCACAAAG AGGATTAGTC 1241 GCTTTGGCTC AGGGCTGCCA GGAGCTAGAA TACATGGCGG 1281 TGTATGTCTC AGATATAACC AACGAGTCTC TCGAAAGCAT 1321 AGGCACATAT CTGAAAAACC TCTGTGACTT CCGCCTCGTC 1361 TTACTCGACC AAGAAGAGAG AATAACAGAT CTGCCACTAG 1401 ACAACGGAGT CCGATCCCTC TTGATCGGAT GCAAGAAACT 1441 CAGACGGTTT GCATTCTATC TCAGACAAGG CGGCTTAACA 1481 GACGTGGGGT TAAGCTACAT CGGACAGTAC AGTCCAAACG 1521 TGAGGTGGAT GCTTCTCGGT TACGTTGGTG AATCAGACGA 1561 AGGCCTAATG GAGTTCTCAA GAGGATGTCC GAAACTACAG 1601 AAGCTGGAGA TGAGAGGTTG TTGCTTCAGC GAGCGAGCAA 1641 TAGCTGCAGC GGTACTGAAA ATCCCTTCGC TGAGATACCT 1681 GTGGGTACAA GGCTACAGAG CATCAACGAC GGGACAAGAC 1721 CTGAGGCTAA TGTCTAGACC GTACTGGAAC ATCGAGCTGA 1761 TTCCGGCAAG AAAAGTCCCA GAAGTGAATC AGCTTGGAGA 1801 GGTGAGAGAG ATGGAGCATC CTGCTCATAT ACTGGCTTAC 1841 TACTCTCTGG CTGGTGAGAG AACAGATTGT CCACCAACTG 1881 TTAAAGTCCT GAGGGAGGCA TGATGATGAT GATGATGATG 1921 ATGAAAAGCA GGTTTGTACA TAAAGATTTG GTTTTGAGGT 1961 TTCCACGAAC TGTCGAATGG ATTCTATTTT TCTTTATTGG 2001 TGTATTGTCT GTAGTTTTGA GAGATTCCAT AAAGACTTTT 2041 GAGAGATTGA AATAAGAAGA GAGAAAACTA GTCTATTCAG 2081 AAGA

An example of a COI1 protein from Theobroma cacao (cocoa) with NCBI accession number XP_007009091.2 (GI:1063526274) has the following sequence (SEQ ID NO:12).

1 MEENDNKMNK TMTSPVGMSD VVLGCVMPYI HDPKDRDAVS 41 LVCRRWYELD ALTRKHITIA LCYTTSPDRL RRRFQHLESL 81 KLKGKPRAAM FNLIPEDWGG YVTPWVNEIA ENFNCLKSLH 121 FRRMIVKDSD LEVLARSRGK VLQVLKLDKC SGFSTDGLLH 161 VGRSCRQLKT LFLEESLIVE KDGQWLHELA VNNSVMETLN 201 FYMTDLVKVS FEDLELIARN CRNLASVKIS DCEILDLVGF 241 FPAAAVLEEF CGGSFNEQPD RYHAVSFPPK LCRLGLTYMG 281 KNEMPIVFPF ASLLKKLDLL YALLDTEDHC LLIQRCPNLE 321 VLETRNVIGD RGLEVLARSC KRLKRLRIER GADEQGMEDE 361 EGVVSQRGLM ALAQGCLELE YL A VYVSDIT NASLEYIGTY 401 SKNLSDFRLV LLDREERITD LPLDNGVRAL LRGCEKLRRF 441 ALYLRPGGLT DVGLSYIGQY SPNVRWMLLG YVGESDAGLL 481 EFSKGCPSLQ KLEMRGCCFS EHALAVTVMQ LTSLRYLWVQ 521 GYRASQSGRD LLAMARPFWN IELIPARRVV MNDQVGEAVV 561 VEHPAHILAY YSLAGPRTDF PETVIPLDPL VAA

A comparison of the Arabidopsis thaliana COI1 SEQ ID NO:1 sequence and the Theobroma cacao COI1 SEQ ID NO:12 sequence is shown below, illustrating that the two proteins have at least 73% sequence identity. In addition, the location of the alanine at position 384 that can be replaced, for example with a valine, to generate a modified COI1 protein is also identified in bold and with underlining. As illustrated, this alanine is at about position 383 in the Theobroma cacao COI1 SEQ ID NO:12 sequence.

73.1% identity in 583 residues overlap; Score: 2221.0; Gap frequency: 0.5% Seq1 3 DPDIKRCKLSCVATVDDVIEQVMTYITDPKDRDSASLVCRRWFKIDSETREHVTMALCYT Seq12 5 DNKMNKTMTSPVGMSDVVLGCVMPYIHDPKDRDAVSLVCRRWYELDALTRKHITIALCYT *        * *   * *   ** ** ******  *******   *  ** * * ***** Seq1 63 ATPDRLSRRFPNLRSLKLKGKPRAAMFTLIPENWGGYVTPWVTEISNNLRQLKSVHFRRM Seq12 65 TSPDRLRRRFQHLESLKLKGKPRAAMFNLIPEDWGGYVTPWVNEIAENFNCLKSLHFRRM   **** ***  * ****************** ********* **  *   *** ***** Seq1 123 IVSDLDLDRLAKARADDLETLKLDKCSGFTTDGLLSIVTHCRKIKTLLMEESSFSEKDGK Seq12 125 IVKDSDLEVLARSRGKVLQVLKLDKCSGFSTDGLLHVGRSCRQLKTLFLEESLIVEKDGQ ** * **  **  *   *  ********* *****     **  ***  ***   **** Seq1 183 WLHELAQHNTSLEVLNFYMTEFAKISPKDLETIARNCRSLVSVKVGDFEILELVGFFKAA Seq12 185 WLHELAVNNSVMETLNFYMTDLVKVSFEDLELIARNCRNLASVKISDCEILDLVGFFPAA ******  *   * ******   * *  *** ****** * ***  * *** ***** ** Seq1 243 ANLEEFCGGSLNEDIGMPEKYMNLVFPRKLCRLGLSYMGPNEMPILFPFAAQIRKLDLLY Seq12 245 AVLEFFCGGSFNEQ---PDRYHAVSFPPKLCRLGLTYMGKNEMPIVFPFASLLKKLDLLY * ******** **    *  *    ** ******* *** ***** ****    ****** Seq1 303 ALLETEDHCTLIQKCPNLEVLETRNVIGDRGLEVLAQYCKQLKRLRIERGADEQGMEDEE Seq12 302 ALLDTEDHCLLIQRCPNLEVLETRNVIGDRGLEVLARSCKRLKRLRIERGADEQGMEDEE *** ***** *** ********************** ** ******************* Seq1 363 GLVSQRGLIALAQGCQELEYM A VYVSDITNESLESIGTYLKNLCDFRLVLLDREERITDL Seq12 362 GVVSQRGLMALAQGCLELEYL A VYVSDITNASLEYIGTYSKNLSDFRLVLLDREERITDL * ****** ****** **** ********* *** **** *** **************** Seq1 423 PLDNGVRSLLIGCKKLRRFAFYLKGGLTDLGLSYIGQYSPNVRWMLLGYVGESDEGLME Seq12 422 PLDNGVRALLRGCEKLRRFALYLRPGGLTDVGLSYIGQYSPNVRWMLLGYVGESDAGLLE ******* ** ** ****** *** ***** ************************ ** * Seq1 483 FSRGCPNLQKLEMRGCCFSERAIAAAVTKLPSLRYLWVQGYRABMTGQDLMQMARPYWNI Seq12 482 FSKGCPSLQKLEMRGCCFSEHALAVTVMQLTSLRYLWVQGYRASQSGRDLLAMARPFWNI ** *** ************* * *  *  * *************  * **  **** *** Seq1 543 ELIPSRRVPEVNQQGEIREMEHPAHILAYYSLAGQRTDCPTTV Seq12 542 ELIPARRVVMNDQVGEAVVVEHPAHILAYYSLAGPRTDFPETV **** ***    * **    ************** *** * **

A modified COI1 Theobroma cacao (cocoa) protein with a valine instead of the alanine at position 383 (of SEQ ID NO: 12) has the following sequence (SEQ ID NO:13).

1 MEENDNKMNK TMTSPVGMSD VVLGCVMPYI HDPKDRDAVS 41 LVCRRWYELD ALTRKHITIA LCYTTSPDRL RRRFQHLESL 81 KLKGKPRAAM FNLIPEDWGG YVTPWVNEIA ENFNCLKSLH 121 FRRMIVKDSD LEVLARSRGK VLQVLKLDKC SGFSTDGLLH 161 VGRSCRQLKT LFLEESLIVE KDGQWLHELA VNNSVMETLN 201 FYMTDLVKVS FEDLELIARN CRNLASVKIS DCEILDLVGF 241 FPAAAVLEEF CGGSFNEQPD RYHAVSFPPK LCRLGLTYMG 281 KNEMPIVFPF ASLLKKLDLL YALLDTEDHC LLIQRCPNLE 321 VLETRNVIGD RGLEVLARSC KRLKRLRIER GADEQGMEDE 361 EGVVSQRGLM ALAQGCLELE YL V VYVSDIT NASLEYIGTY 401 SKNLSDFRLV LLDREERITD LPLDNGVRAL LRGCEKLRRF 441 ALYLRPGGLT DVGLSYIGQY SPNVRWMLLG YVGESDAGLL 481 EFSKGCPSLQ KLEMRGCCFS EHALAVTVMQ LTSLRYLWVQ 521 GYRASQSGRD LLAMARPFWN IELIPARRVV MNDQVGEAVV 561 VEHPAHILAY YSLAGPRTDF PETVIPLDPL VAA

An example of a nucleotide (cDNA) sequence that encodes the Theobroma cacao SEQ ID NO: 12 COI1 protein (NCBI cDNA accession number XM_007009029.2 (GI:1063526273) is shown below as SEQ ID NO:14.

1 AAGTTTCAGC TCTCCTTCTC TGTTTCACGT TTCTGTGGGC 41 GCTCTCTACT CTGCCATGCC TTCTCTACAC GACCCATTTT 81 TGACCCGATT CGTTTAGCCC CGGGGGAAAT TTGCTTCGTT 121 TCAGATCCTA CCGCCGTTTC GTTTCTTCCA CTTCCGTAAA 161 AGAGAAGAGT TCCACGCCCG TTTCTTCTTC TTCTTCTTCT 201 TCAGATCAGT CTTTTTTTTT TTTTGCCGTT TCGCGTTTCT 241 GGTTTATTTG GGCTGAAAAG ATCCGATTCG ATTGTATTGA 281 ATGGAGGAAA ATGATAACAA GATGAACAAA ACGATGACGT 321 CACCAGTCGG TATGTCGGAC GTCGTTTTAG GCTGCGTGAT 361 GCCGTACATC CACGACCCGA AAGACCGGGA CGCAGTTTCG 401 CTCGTGTGCC GACGTTGGTA CGAGCTCGAC GCGTTGACGA 441 GGAAGCACAT AACGATCGCG CTTTGCTACA CGACGAGTCC 481 CGATCGGTTG CGACGTCGTT TCCAGCACTT GGAATCTTTG 521 AAGTTGAAAG GCAAGCCTCG GGCGGCGATG TTCAATTTGA 561 TACCTGAGGA TTGGGGAGGG TACGTGACGC CGTGGGTGAA 601 TGAGATAGCT GAGAATTTTA ATTGCTTGAA ATCTTTGCAT 641 TTTAGAAGGA TGATTGTTAA AGATTCGGAT CTGGAAGTTT 681 TGGCTCGGTC TAGAGGGAAG GTTTTGCAGG TTTTGAAGCT 721 TGATAAATGC TCTGGTTTCT CTACTGATGG TCTCTTGCAC 761 GTTGGACGCT CCTGCCGGCA ATTAAAAACC TTGTTCCTGG 801 AAGAGAGCTT AATTGTTGAG AAAGATGGTC AATGGCTTCA 841 TGAGCTTGCA GTAAATAACT CAGTTATGGA GACTTTGAAC 881 TTTTATATGA CAGATCTTGT CAAAGTGAGT TTTGAAGACC 921 TTGAACTTAT TGCTAGAAAT TGTCGCAACT TGGCCTCTGT 961 GAAAATTAGC GATTGTGAAA TTTTGGATCT TGTTGGTTTC 1001 TTTCCTGCTG CTGCTGTTTT AGAAGAATTT TGTGGTGGTT 1041 CTTTCAATGA GCAACCGGAT AGGTACCATG CTGTATCATT 1081 CCCCCCAAAG TTATGCCGTT TGGGTTTAAC ATACATGGGG 1121 AAGAATGAAA TGCCAATTGT GTTCCCTTTT GCATCCTTGC 1161 TTAAAAAGTT GGATCTCCTC TATGCATTAC TTGACACAGA 1201 AGACCACTGC TTGTTAATTC AGAGATGCCC CAACTTAGAA 1241 GTTCTTGAGA CAAGGAATGT TATTGGAGAT AGAGGATTAG 1281 AAGTTCTTGC TCGAAGTTGT AAGAGACTAA AGAGGCTTAG 1321 AATTGAAAGG GGTGCTGATG AGCAGGGAAT GGAGGATGAA 1361 GAAGGTGTGG TTTCACAAAG AGGATTAATG GCTTTAGCTC 1401 AGGGATGCCT TGAATTGGAA TACTTGGCTG TTTATGTATC 1441 TGACATCACC AATGCATCAT TGGAATACAT TGGGACTTAC 1481 TCAAAAAATC TCTCTGATTT TCGCCTAGTC TTGCTTGACC 1521 GAGAAGAAAG GATAACAGAT TTGCCTCTTG ATAATGGAGT 1561 CCGGGCTCTA TTGAGGGGCT GTGAAAAGCT TAGAAGATTT 1601 GCTCTGTACC TCCGACCTGG TGGTTTGACT GATGTAGGCC 1641 TCAGTTATAT TGGGCAATAC AGTCCGAATG TAAGATGGAT 1681 GCTTCTAGGT TATGTTGGGG AGTCGGATGC CGGGCTTTTG 1721 GAGTTCTCTA AGGGATGCCC AAGCCTGCAG AAACTAGAAA 1761 TGAGGGGTTG TTGCTTCAGT GAGCATGCAC TTGCAGTTAC 1801 TGTGATGCAA TTAACTTCCT TGAGGTATTT GTGGGTGCAA 1841 GGATATAGAG CGTCACAATC AGGTCGTGAT CTTTTAGCAA 1881 TGGCTCGTCC ATTTTGGAAT ATCGAGCTAA TTCCTGCAAG 1921 ACGAGTAGTT ATGAATGATC AGGTTGGAGA GGCTGTTGTG 1961 GTTGAGCATC CGGCTCATAT ACTCGCGTAT TACTCCCTAG 2001 CTGGACCAAG AACAGATTTT CCAGAAACTG TTATTCCTTT 2041 GGATCCATTA GTTGCTGCGT AGAGCTGTAA ATATGACCTA 2081 TTTTTCGAAG TGTCCATTTT TCCCATCCAC GTTCTGTCTA 2121 TAAAGTTTCT GCACCTTTCT CTTTTCTCTT TTCCTTTCCT 2161 TTTTGTTTAG AGGGTTTCCA ATTTGATATT TCATTTTCGA 2201 TTTTATTTCT AGACTTTGTC CTGTAATAAG ATTGTGTTTT 2241 CTTCTGTAAT TTTGAAAGCA CTTGCACTCT TGGTGGGCTA 2281 CTGTTTTTGT CCCTTGTCCC TGGAAAAAGT AGTGAATGAC 2321 TCTTAACGGA ATA

An example of a COI1 protein from Prunus persica (peach) with NCBI accession number XP_007220435.1 (GI:596048914) has the following sequence (SEQ ID NO:15).

1 MEDRNVRSGM SDVVIGCVMP YLHDAKDRDA VSLVCRRWYE 41 LDALTRKHVT IALCYTTSPD RLRRRFQHLE SLKLKGKPRA 81 AMFNLIPEDW GGFVTPWVKE IAESFNRLKS LHFRRMIVKD 121 SDLELLAQSR GRVLQALKLD KCSGFSTDGL LHIGRSCRNL 161 RTLFLEESSI DENDGQWLHE LALNNSVLET LNFYMTDLIK 201 VKFEDLELIA KNCRSLTSVK TSDCEILELV GFFRSASVLE 241 EFCGGFFNEQ SERYSVVSLP QKLCRLGLTY MGKNEMPIVF 281 PYATLLKKLD LLYALLDTED HCTLIQRCPN LEVLETRNVI 321 GDRGLEVLAR SCKRLRRLRI ERGADEQGME DEEGVVSQRG 361 LIALAQGCLE LEYL A VYVSD ITNASLEFIG TYSKNLCDFR 401 LVLLDREETI TDLPLDNGVR ALLRGCDKLR RFALYLRAGG 441 LTDLGLSYVG QYSQNVRWML LGYVGESDAG LLEFSKGCPS 481 LQKLEMRGCC FSERALADAV MQLTSLRYLW VQGYRGSASG 521 RDVLAMARPY WNIELIPPRR VVDQQGEGVV MEHPAHILAY 561 YSLAGQRTDY PNTVIPVDPA SFITS

A comparison of the Arabidopsis thaliana COI1 SEQ ID NO:1 sequence and the Prunus persica COI1 SEQ ID NO:15 sequence is shown below, illustrating that the two proteins have at least 73% sequence identity. In addition, the location of the alanine at position 384 that can be replaced, for example with a valine, to generate a modified COI1 protein is also identified in bold and with underlining. As illustrated, this alanine is at about position 375 in the Prunus persica COI1 SEQ ID NO:15 sequence.

74.3% identity in 568 residues overlap; Score: 2187.0; Gap frequency: 0.9% Seq1 18 DDVIEQVMTYITDPKDRDSASLVCRRWFKIDSETREHVTMALCYTATPDRLSRRFPNLRS Seq15 12 DVVIGCVMPYLHDAKDRDAVSLVCRRWYELDALTRKHVTIALCYTTSPDRLRPRFQHLES * **  ** *  * ****  *******   *  ** *** *****  **** ***  * * Seq1 78 LKLKGKPRAAMFNLIPENWGGYVTPWVTEISNNLRQLKSVHFRRMIVSDLDLDRLAKARA Seq15 72 LKLKGKPRAAMFNLIPEDWGGEVTPWVKEIAESFNRLKSLHFRRMIVKDSDLELLAQSRG ***************** *** ***** **      *** ******* * **  **  * Seq1 138 DDLETLKLDKCSGFTTDGLLSIVTHCRKIKTLLMEESSFSEKDGKWLHELAQHNTSLEVL Seq15 132 RVLQALKLDKCSGFSTDGLLHIGRSCRNLRTLFLEESSIDENDGQWLHELALNNSVLETL   *  ********* ***** *   **   **  ****  * ** ******  *  ** * Seq1 198 NFYMTEFAKISPKDLETIARNCRSLVSVKVGDFEILELVGFFKAAANLEEFCGGSLNEDI Seq15 192 NFYMTDLIKVKFEDLELIAKNCRSLTSVKTSDCEILELVGFFRSASVLEEFCGGFFNEQ- *****   *    *** ** ***** ***  * *********  *  *******  ** Seq1 258 GMPEKYMNVFPRKLCRLGLSYMGPNEMPILFPFAAQIRKLDLLYALLETEDHCTLIQKC Seq15 251 -SERYSVVSLPQKLCRLGLTYMGKNEMPIVFPYATLLKKLDLLYALLDTEDHCTLIQRC    * *     * ******* *** ***** ** *    ********* ********* * Seq1 318 PNLEVLETRNVIGDRGLEVLAQYCKQLKRLRIERGADEQGMEDEEGLVSQRGLIALAQGC Seq15 309 PNLEVLETRNVIGDRGLEVLARSCKRLRRLRIERGADEQGMEDEEGVVSQRGLIALAQGC *********************  ** * ****************** ************* Seq1 378 QELEYM A VYVSDITNESLESIGTYLKNLCDFRLVLLDREERITDLPLDNGVRSLLIGCKK Seq15 369 LELEYL A VYVSDITNASLEFIGTYSKNLCDFRLVLLDREETITDLPLDNGVRALLRGCDK  **** ********* *** **** *************** *********** ** ** * Seq1 438 LRRFAFYLRQGGLTDLGLSYIGQYSPNVRWMLLGYVGESDEGLMEFSRGCPNLQKLEMRG Seq15 429 LRRFALYLRAGGLTDLGLSYVGQYSQNVRWMLLGYVGESDAGLLEFSKGCPSLQKLEMRG ***** *** ********** **** ************** ** *** *** ******** Seq1 498 CCFSERAIAAAVTKLPSLRYLWVQGYRASMTGQDLMQMARPYWNIELIPSRRVPEVNQQG Seq15 489 CCFSERALADAVMQLTSLRYLWVQGYRGSASGRDVLAMARPYWNIELIPPRRV--VDQQG ******* * **  * *********** *  * *   ************ ***  * *** Seq1 558 EIREMEHPAHILAYYSLAGQRTDCPTTV Seq15 547 EGVVMEHPAHILAYYSLAGQRTDYPNTV *   ******************* * **

An example of a modified COI1 Prunus persica (peach) protein with a valine instead of an alanine at position 375 has the following sequence (SEQ ID NO:16).

1 MEDRNVRSGM SDVVIGCVMP YLHDAKDRDA VSLVCRRWYE 41 LDALTRKHVT IALCYTTSPD RLRRRFQHLE SLKLKGKPRA 81 AMFNLIPEDW GGFVTPWVKE IAESFNRLKS LHFRRMIVKD 121 SDLELLAQSR GRVLQALKLD KCSGFSTDGL LHIGRSCRNL 161 RTLFLEESSI DENDGQWLHE LALNNSVLET LNFYMTDLIK 201 VKFEDLELIA KNCRSLTSVK TSDCEILELV GFFRSASVLE 241 EFCGGFFNEQ SERYSVVSLP QKLCRLGLTY MGKNEMPIVF 281 PYATLLKKLD LLYALLDTED HCTLIQRCPN LEVLETRNVI 321 GDRGLEVLAR SCKRLRRLRI ERGADEQGME DEEGVVSQRG 361 LIALAQGCLE LEYL V VYVSD ITNASLEFIG TYSKNLCDFR 401 LVLLDREETI TDLPLDNGVR ALLRGCDKLR RFALYLRAGG 441 LTDLGLSYVG QYSQNVRWML LGYVGESDAG LLEFSKGCPS 481 LQKLEMRGCC FSERALADAV MQLTSLRYLW VQGYRGSASG 521 RDVLAMARPY WNIELIPPRR VVDQQGEGVV MEHPAHILAY 561 YSLAGQRTDY PNTVIPVDPA SFITS

An example of a nucleotide (cDNA) sequence that encodes the Prunus persica SEQ ID NO:15 COI1 protein (NCBI cDNA accession number XM_007220373.1 (GI:596048913)) is shown below as SEQ ID NO:17.

1 ATGGAGGATC GAAACGTGCG AAGTGGAATG TCCGATGTGG 41 TGATAGGCTG CGTGATGCCG TATCTTCACG ACGCTAAGGA 81 CCGCGACGCA GTGTCGTTGG TGTGCCGGCG ATGGTACGAG 121 CTCGACGCTC TCACGCGCAA GCACGTGACC ATTGCTCTCT 161 GCTACACCAC GAGCCCCGAT CGGTTGCGGA GGCGATTTCA 201 GCACCTCGAG TCCCTGAAGC TGAAAGGGAA GCCGAGAGCG 241 GCGATGTTCA ATCTGATACC GGAGGATTGG GGAGGCTTTG 281 TGACGCCGTG GGTGAAGGAG ATCGCTGAGT CCTTCAATCG 321 CTTGAAGTCT CTGCACTTTC GGCGAATGAT TGTTAAGGAT 361 TCGGACTTGG AGCTCTTGGC TCAGTCCCGT GGGCGCGTGC 401 TACAGGCGCT CAAGCTTGAC AAGTGCTCTG GCTTCTCCAC 441 CGATGGCCTT TTGCACATCG GCCGCTCCTG CAGGAATTTG 481 AGAACCTTGT TTTTGGAAGA GAGCTCCATA GATGAGAATG 521 ATGGTCAATG GCTACATGAG CTTGCTTTGA ACAACTCTGT 561 GTTGGAGACT TTGAATTTTT ATATGACAGA TCTTATCAAA 601 GTCAAATTTG AAGACCTTGA ACTCATTGCA AAAAACTGTC 641 GCTCCTTAAC CTCTGTGAAA ACTAGCGATT GCGAAATCTT 681 GGAACTCGTG GGCTTCTTCC GTTCTGCAAG CGTATTAGAA 721 GAATTTTGTG GCGGTTTCTT CAACGAGCAA TCAGAGAGGT 761 ACTCTGTTGT ATCGTTACCC CAAAAATTAT GCCGTTTGGG 801 TCTAACGTAC ATGGGAAAGA ATGAAATGCC AATAGTATTC 841 CCATATGCAA CCCTTCTCAA AAAGCTGGAT CTCCTTTATG 881 CATTGCTCGA CACTGAGGAC CATTGCACAC TAATTCAAAG 921 GTGCCCCAAC CTGGAAGTGC TTGAGACAAG GAATGTTATT 961 GGAGATAGAG GACTAGAAGT TCTTGCTCGG AGTTGCAAGA 1001 GATTGAGGAG GCTCCGAATT GAGCGAGGTG CAGATGAGCA 1041 AGGCATGGAG GATGAAGAAG GTGTTGTTTC ACAAAGGGGT 1081 TTGATAGCAT TGGCACAGGG CTGCCTGGAA CTTGAGTACT 1121 TGGCTGTGTA TGTGTCAGAT ATCACAAACG CATCTCTGGA 1161 ATTCATTGGG ACTTACTCTA AGAATCTTTG TGATTTTCGA 1201 CTTGTCTTGC TTGACCGAGA AGAGACGATA ACAGATTTAC 1241 CACTTGACAA TGGGGTTCGA GCTCTTTTGA GGGGCTGTGA 1281 TAAGCTCAGA AGGTTTGCTC TGTATCTCCG TGCTGGGGGC 1321 TTGACCGATT TGGGACTTAG TTATGTTGGC CAGTATAGTC 1361 AAAATGTGAG ATGGATGCTT CTGGGTTATG TTGGGGAATC 1401 TGATGCAGGG CTTTTGGAGT TCTCTAAAGG TTGCCCTAGC 1441 CTGCAAAAAT TGGAAATGAG GGGCTGTTGC TTCAGTGAGC 1481 GTGCACTGGC TGATGCAGTA ATGCAGCTGA CTTCCCTTAG 1521 GTACTTGTGG GTGCAGGGGT ACAGAGGATC TGCTTCGGGT 1561 CGTGATGTTT TGGCAATGGC TCGGCCGTAT TGGAATATTG 1601 AGTTAATTCC CCCGAGACGA GTTGTTGATC AGCAGGGGGA 1641 GGGAGTAGTG ATGGAGCATC CAGCCCATAT ACTTGCATAC 1681 TACTCACTTG CTGGACAAAG AACAGATTAT CCAAATACTG 1721 TTATCCCCGT GGATCCAGCA TCTTTTATTA CCTCCTAGAG 1761 TT

An example of a COI1 protein from Malus domestica (apple) with NCBI accession number XP_008392915.1 (GI:658000912) has the following sequence (SEQ ID NO:18).

1 MEDRSVRCRI SDVVMDCVMP YLHDPKDRDA VSLVCKRWYE 41 LDALTRKHVT IALCYTTTPD RLRQRFQHLE SLKLKGKPRA 81 AMFNLIPEDW GGFVTPWVME IANSFHRLKC LHFRRMIVSD 121 SDLELLADSR GRVLQVLKLD KCSGFTTGGL LHIGRSCRNL 161 RTLFLEESSI VEEDGDWLHA LAVNNTVLET LNFYMTDLIK 201 VKFEDLELIA KNCRSLTSVK ISDCEILELV GFFRHAAVLE 241 EFCGGSFNDQ SESYSVVTLP QKLCRLGLTY MGKNEMQIVF 281 PFATLLKKLD LLYALLDTED HCTLIQRCPN LEVLETRNVI 321 GDRGLDVLAR SCKRLRRLRI ERGADEGMED EEGVVSQRGL 361 MALAQGCLEL E YLAVYVSDI TNASLEYIGT YSKNLSDFRL 401 VLLDREETIT DLPLDNGVRA LLRGCHKLRR FALYLRPGGL 441 TDLGLSYIGR YSPNVRWMLL GYVGESDAGL LEFSKGCPSL 481 QKLEMRGCCF SERALAHAVM QLTSLRYLWV QGYRGSATGR 521 DLLAMARPFW NIELIPPRRV DVPDQHGEAL AVEHPAHILA 561 YYSLAGPRTD CPDTVIPVDP ASLLIS

A comparison of the Arabidopsis thaliana COI1 SEQ ID NO:1 sequence and the Malus domestica (apple) COI1 SEQ ID NO:18 sequence is shown below, illustrating that the two proteins have at least 72% sequence identity. In addition, the location of the alanine at position 384 that can be replaced, for example with a valine, to generate a modified COI1 protein is also identified in bold and with underlining. As illustrated, this alanine is at about position 374 in the Malus domestica COI1 SEQ ID NO:18 sequence.

73.6% identity in 568 residues overlap; Score: 2171.0; Gap frequency: 0.7% Seq1 18 DDVIEQVMTYITDPKDRDSASLVCRRWFKIDSETREHVTMALCYTATPDRLSRRFPNLRS Seq18 12 DVVMDCVMPYLHDPKDRDAVSLVCKRWYELDALTRKHVTIALGYTTTPDRLRQRFQHLES * *   ** *  ******  **** **   *  ** *** ***** *****  **  * * Seq1 78 LKLKGKPRAAMFNLIPENWGGYVTPWVTEISNNLRQLKSVHFRRMIVSDLDLDRLAKARA Seq18 72 LKLKGKPRAAMFNLIPEDWGGFVTPWVMEIANSFHRLKCLHFRRMIVSDSDLELLADSRG ***************** *** ***** ** *    **  ********* **  **  * Seq1 138 DDLETLKLDKCSGFTTDGLLSIVTHCRKIKTLLMEESSFSEKDGKWLHELAQHNTSLEVL Seq18 132 RVLQVLKLDKCSGFTTGGLLHIGRSCRNLRTLFLEESSIVEEDGDWLHALAVNNTVLETL   *  *********** *** *   **   **  ****  * ** *** **  ** ** * Seq1 198 NFYMTEFAKISPKDLETIARNCRSLVSVKVGDFEILELVGFFKAAANLEEFCGGSLNEDI Seq18 192 NFYMTDLIKVKFEDLELIAKNCRSLTSVKISDCEILELVGFFRHAAVLEEFCGGSFNDQ- *****   *    *** ** ***** ***  * *********  ** ******** * Seq1 258 GMPEKYMNLVFPRKLCRLGLSYMGPNEMPILFPFAAQIRKLDLLYALLETEDHCTLIQKC Seq18 251 --SESYSVVTLPQKLCRLGLTYMGKNEMQIVFPFATLLKKLDLLYALLDTEDHCTLIQRC    * *     * ******* *** *** * ****    ********* ********* * Seq1 318 PNLEVLETRNVIGDRGLEVLAQYCKQLKRLRIERGADEQGMEDEEGLVSQRGLIALAQGC Seq18 309 PNLEVLETRNVIGDRGLDVLARSCKRLRRLRIERGADE-GMEDEEGVVSQGLMALAQGC ***************** ***  ** * ********** ******* ****** ****** Seq1 378 QELEYM A VYVSDITNESLESIGTYLKMLCDFRLVLLDREERITDLPLDNGVRSLLIGCKK Seq18 368 LELEYL A VYVSDITNASLEYIGTYSKMLSDFRLVLLDREETITDLPLDNGVRALLRGCHK  **** ********* *** **** *** *********** *********** ** ** * Seq1 438 LRRFAFYLRQGGLTDLGLSYIGQYSPNVRWMLLGYVGESDEGLMEFSRGCPNLQKLEMRG Seq18 428 LRRFALYLRPGGLTDLGLSYIGRYSPNVRWMLLGYVGESDAGLLEFSKGCPSLQKLEMRG ***** *** ************ ***************** ** *** *** ******** Seq1 498 CCFSERAIAAAVTKLPSLRYLWVQGYRASMTGQDLMQMARPYWNIELIPSRRVPEVNQOG Seq18 488 CCFSERALAHAVMQLTSLRYLWVQGYRGSATGRDLLAMARPFWNIELIPPRRVDVPDQHG ******* * **  * *********** * ** **  **** ******* ***   * * Seq1 658 EIREMEHPAHILAYYSLAGQRTDCPTTV Seq18 548 EALAVEHPAHILAYYSLAGPRTDCPDTV *    ************** ***** **

An example of a modified Malus domestica (apple) COI1 protein with a valine instead of a glutamic acid at about position 374 has the following sequence (SEQ ID NO:19).

1 MEDRSVRCRI SDVVMDCVMP YLHDPKDRDA VSLVCKRWYE 41 LDALTRKHVT IALCYTTTPD RLRQRFQHLE SLKLKGKPRA 81 AMFNLIPEDW GGFVTPWVME IANSFHRLKC LHFRRMIVSD 121 SDLELLADSR GRVLQVLKLD KCSGFTTGGL LHIGRSCRNL 161 RTLFLEESSI VEEDGDWLHA LAVNNTVLET LNFYMTDLIK 201 VKFEDLELIA KNCRSLTSVK ISDCEILELV GFFRHAAVLE 241 EFCGGSFNDQ SESYSVVTLP QKLCRLGLTY MGKNEMQIVF 281 PFATLLKKLD LLYALLDTED HCTLIQRCPN LEVLETRNVI 321 GDRGLDVLAR SCKRLRRLRI ERGADEGMED EEGVVSQRGL 361 MALAQGCLEL V YLAVYVSDI TNASLEYIGT YSKNLSDFRL 401 VLLDREETIT DLPLDNGVRA LLRGCHKLRR FALYLRPGGL 441 TDLGLSYIGR YSPNVRWMLL GYVGESDAGL LEFSKGCPSL 481 QKLEMRGCCF SERALAHAVM QLTSLRYLWV QGYRGSATGR 521 DLLAMARPFW NIELIPPRRV DVPDQHGEAL AVEHPAHILA 561 YYSLAGPRTD CPDTVIPVDP ASLLIS

An example of a nucleotide (cDNA) sequence that encodes the Malts domestica SEQ ID NO:18 COI1 protein (NCBI cDNA accession number XM_008394693.2 (GI:1039847064)) is shown below as SEQ ID NO:20.

1 GCCCGCTTCC CTTTTCAATC CCCCCTCCCT TATGTGTTTG 41 TGAGGCGCAT AATTATTCTT GAACACCACT AATAACTGAA 81 AGTCCGATCC AATAGCCGCC GGATTCCTCC CCGGACGATC 121 CCCACCGTAC GTTTCAGATC CGTCTTCTCA GACCATGTGC 161 TTCGAGTCCA CGCCGACTCC ATGCTCCGGC GCTCCTCCAC 201 TGGTCGCCCT GCTCCGCCGT CTTCGATCCG ATTGGTCTGT 241 TTTCTGCGCG AGCTTCTCGT AGATCGTGCT TTCTAGCTCC 281 TCTCTCTTCC CTCTTGTTCC TGCTCGTTTC TTGACACGTT 321 GCGGCGTTTC TCTGAGATTC TGATTCTGTA AACGTCGGTG 361 CCACGGTGTC CTTTTAGTTC TTTTTTTTGA TTGGATTTGG 401 AAATATAACA GCTTAGGGTT CCGATTTTGG AAATCCAGTT 441 TCTATTTCTG GAAATATTTG GAGTTGAGGA TTCGGAGCTC 481 CGAAAACCCG ATCTTGAGAG AATTCGAATC TTTTTCCACT 521 TTTGACTCTG AAATTTTTTT GTTAGAAATA GCAGTAGAGT 561 TTTTTCAGTG AGTATTTTCA TCGCCGACGT TTCTTTTTAG 601 CGATGGAGGA TCGAAGCGTG CGGTGTAGGA TTTCCGACGT 641 CGTAATGGAC TGCGTGATGC CGTATCTCCA CGACCCCAAG 681 GACCGTGACG CCGTGTCGTT GGTGTGCAAG CGGTGGTACG 721 AGCTCGACGC GCTCACGCGG AAGCACGTGA CCATCGCGCT 761 CTGCTACACC ACGACCCCGG ATCGGCTGCG GCAGCGGTTT 801 CAGCACCTGG AGTCGCTGAA GCTGAAGGGG AAGCCGAGGG 841 CGGCGATGTT CAATCTGATT CCCGAGGACT GGGGAGGGTT 881 TGTAACGCCG TGGGTGATGG AGATCGCCAA CTCGTTCCAC 921 CGCTTGAAGT GTCTGCACTT TCGGCGGATG ATTGTTAGTG 961 ATTCGGACCT GGAGCTCCTG GCTGACTCAC GTGGGCGCGT 1001 GCTTCAGGTG CTTAAGCTCG ACAAGTGCTC AGGGTTTACC 1041 ACCGGTGGGC TTTTGCACAT CGGCCGCTCC TGCAGGAATT 1081 TGAGGACCTT GTTTTTGGAA GAGAGCTCCA TAGTTGAGGA 1121 AGATGGCGAC TGGCTACACG CGCTTGCTGT AAACAATACT 1161 GTCCTGGAGA CTCTGAATTT TTATATGACC GATCTTATCA 1201 AAGTCAAATT CGAAGACCTT GAACTGATAG CCAAAAACTG 1241 CCGCTCCTTA ACCTCTGTGA AAATTAGTGA TTGCGAAATC 1281 TTGGAACTGG TTGGCTTCTT CCGTCATGCA GCTGTCTTGG 1321 AAGAATTTTG TGGGGGTTCC TTCAACGATC AATCCGAGAG 1361 TTACTCTGTT GTAACGTTAC CCCAAAAACT TTGCCGTCTC 1401 GGTCTAACAT ACATGGGAAA GAATGAAATG CAAATAGTGT 1441 TCCCATTTGC AACCCTTCTC AAAAAGCTCG ATCTCCTTTA 1481 TGCATTGCTG GACACTGAGG ACCATTGCAC ATTAATTCAG 1521 AGGTGCCCCA ACCTGGAAGT TCTGGAGACA AGGAATGTTA 1561 TTGGAGATAG AGGACTAGAT GTTCTTGCTC GGAGTTGCAA 1601 GAGACTAAGG AGGCTCCGAA TTGAGCGGGG TGCAGATGAA 1641 GGCATGGAGG ACGAAGAAGG TGTTGTTTCC CAACGGGGTC 1681 TGATGGCCCT GGCGCAGGGA TGCCTAGAGC TCGAATACCT 1721 GGCTGTTTAT GTATCGGACA TCACCAATGC ATCTCTGGAA 1761 TACATTGGGA CTTACTCCAA AAATCTCTCT GATTTTCGCC 1801 TTGTCTTACT TGACCGGGAA GAGACAATAA CAGATTTGCC 1841 ACTTGACAAT GGGGTTCGAG CACTTTTGAG GGGATGCCAT 1881 AAGCTTCGAA GGTTTGCTCT GTATCTCCGT CCTGGGGGGT 1921 TGACTGACCT CGGACTGAGT TACATTGGCC GGTACAGTCC 1961 GAATGTGAGA TGGATGCTTC TGGGTTATGT TGGGGAATCT 2001 GATGCAGGGC TTTTGGAGTT CTCAAAGGGT TGCCCTAGCC 2041 TGCAAAAATT GGAAATGAGG GGTTGCTGCT TCAGCGAGCG 2081 TGCACTCGCT CATGCAGTAA TGCAACTGAC TTCCCTTAGG 2121 TACTTGTGGG TGCAGGGGTA CAGAGGATCT GCTACTGGTC 2161 GCGACCTTTT GGCAATGGCT CGCCCGTTTT GGAATATTGA 2201 GTTGATTCCT CCCAGACGAG TTGATGTTCC TGATCAGCAT 2241 GGGGAGGCAT TAGCGGTCGA GCATCCAGCC CATATACTTG 2281 CATACTACTC ACTTGCTGGA CCGAGAACAG ATTGTCCAGA 2321 TACTGTTATT CCCGTGGATC CGGCATCTTT ACTCATCTCC 2361 TAGAGCTGTA CATACAACCT CTTTTTTTCT TCCACAAGCA 2401 GTCATTTTCT TACCACGCCT TGTTTATAAA TTCATGTAAC 2441 TTTTTTACTT TTGGTTAAGA GGGTTTCGAT TTCAAGTTTC 2481 AATTATATTT CTAGACCTTA GTTCTGTAAT AAGTTTGAGT 2521 TACCCTGTGT AATCTGAAAG CACTTGCACT CTTTGATCCG 2561 GAA

An example of a COI1 protein from Glycine max (soybean) with NCBI accession number NP_001238590.1 (GI:351724347) has the following sequence (SEQ ID NO:21).

1 MTEDRNVRKT RVVDLVLDCV IPYIDDPKDR DAVSQVCRRW 41 YELDSLTRKH VTIALCYTTT PARLRRRFPH LESLKLKGKP 81 RAAMFNLIPE DWGGHVTPWV KEISQYFDCL KSLHFRRMIV 121 KDSDLRNLAR DRGHVLHSLK LDKCSGFTTD GLFHIGRFCK 161 SLRVLFLEES SIVEKDGEWL HELALNNTVL ETLNFYLTDI 201 AVVKIQDLEL LAKNCPNLVS VKLTDSEILD LVNFFKHASA 241 LEEFCGGTYN EEPEKYSAIS LPAKLCRLGL TYIGKNELPI 281 VFMFAAVLKK LDLLYAMLDT EDHCMLIQKC PNLEVLETRN 321 VIGDRGLEVL GRCCKRLKRL RIERGDDDQG MEDEEGTVSH 361 RGLIALSQGC SELEYM A VYV SDITNASLEH IGTHLKNLCD 401 FRLVLLDHEE KITDLPLDNG VRALLRGCNK LRRFALYLRR 441 GGLTDVGLGY IGQYSPNVRW MLLGYVGESD AGLLEFSKGC 481 PSLQKLEMRG CSFFSERALA VAATQLTSLR YLWVQGYGVS 521 PSGRDLLAMA RPFWNIELIP SRKVAMNTNS DETVVVEHPA 561 HILAYYSLAG QRSDFPDTVV PLDTATCVDT

A comparison of the Arabidopsis thaliana COI1 SEQ ID NO:1 sequence and the Glycine max COI1 SEQ ID NO:21 sequence is shown below, illustrating that the two proteins have at least 70% sequence identity. In addition, the location of the alanine at position 384 that can be replaced, for example with a valine, to generate a modified COI1 protein is also identified in bold and with underlining. As illustrated, this alanine is at about position 377 in the Glycine max COI1 SEQ ID NO:21 sequence.

71.8% identity in 570 residues overlap; Score: 2115.0; Gap frequency: 0.7% Seq1 17 VDDVIEQVMTYITDPKDRDSASLVCRRWFKIDSETREHVTMALCYTATPDRLSRRFPNLR Seq21 13 VDLVLDVIPYIDDPKDRDAVSQNCRRWYELDSLTRKHVTIALCYTTTPARLRRRFPHLE ** *   **  ** ****  * *****   ** ** *** ***** ** ** **** * Seq1 77 SLKLKGKPRAAMFNLIPENWGGYVTPWVTEISNNLRQLKSVHFRRMIVSDLDLDRLAKAR Seq21 73 SLKLKGKPRAAMFNLIPEDWGGHVTPWVKEISQYFDCLKSLHFRRMIVKDSDLRNLARDR ****************** *** ***** *** ***    ******* * **  **  * Seq1 137 ADDLETLKLDKCSGFTTDGLLSIVTHCRKIKTLLMEESSFSEKDGKWLHELAQHNTSLEV Seq21 133 GHVLHSLKLDKCSGFTTDGLFHIGRFCKSLRVLFLEESSIVEKDGEWLHELALNNTVLET    *  **************  *   *     *  ****  **** ******  ** ** Seq1 197 LNFYMTEFAKISPKDLETIARNCRSLVSVKVGDFEILELVGFFKAAANLEEFCGGSLNED Seq21 193 LNFYLTDIAVVKIQDLELLAKNCPNLVSVKLTDSEILDLVNFFKHASALEEFCGGTYNEE **** *  *     ***  * **  *****  * *** ** *** *  *******  ** Seq1 257 IGMPEKYMNLVFPRKLCRLGLSYMGPNEMPILFPFAAQIRKLDLLYALLETEDHCTLIQK Seq21 253 ---PEKYSAISLPAKLCRLGLTYIGKNELPIVFMFAAVLKKLDLLYAMLDTEDHCMLIQK    ****     * ******* * * ** ** * ***   ******* * ***** **** Seq1 317 CPNLEVLETRNVIGDRGLEVLAQYCKQLKRLRIERGADEQGMEDEEGLVSQRGLIALAQG Seq21 310 CPNLEVLETRNVIGDRGLEVLGRCCKRLKRLRIERGDDDQGMEDEEGTVSHRGLIALSQG *********************   ** ********* * ******** ** ****** ** Seq1 377 CQELEYM A VYVSDITNESLESIGTYLKYLCDFRLVLLDREERITDLPLDNGVRSLLIGCK Seq21 370 CSELEYM A VYVSDITNASLEHIGTHLKNLCDFRLVLLDHEEKITDLPLDNGVRALLRGCN * ************** *** *** ************* ** *********** ** ** Seq1 437 KLRRFAFYLRQGGLTDLGLSYIGQYSPNVRWMLLGYVGESDEGLMEFSRGCPNLQKLEMR Seq21 430 KLRRFALYLRRGGLTDVGLGYIGQYSPNVRWMLLGYVGESDAGLLEFSKGCPSLQKLEMR ****** *** ***** ** ********************* ** *** *** ******* Seq1 497 GCCF-SERAIAAAVTKLPSLRYLWVQGYRASMTGQDLMQMARPYWNIELIPSRRVPEVNQ Seq21 490 GCSFFSERALAVAATQLTSLRYLWVQGYGVSPSGRDLLAMARPFWNIELIPSRKVAMNTN ** * **** * * * * **********  *  * **  **** ********* * Seq1 556 QGEIREMEHPAHILAYYSLAGQRTDCPTTV Seq21 550 SDETVVVEHPAHILAYYSLAGQRSDFPDTV   *    **************** * * **

An example of a modified Glycine max (soybean) COI1 protein with a valine instead an alanine at about position 377 has the following sequence (SEQ ID NO:22).

1 MTEDRNVRKT RVVDLVLDCV IPYIDDPKDR DAVSQVCRRW 41 YELDSLTRKH VTIALCYTTT PARLRRRFPH LESLKLKGKP 81 RAAMFNLIPE DWGGHVTPWV KEISQYFDCL KSLHFRRMIV 121 KDSDLRNLAR DRGHVLHSLK LDKCSGFTTD GLFHIGRFCK 161 SLRVLFLEES SIVEKDGEWL HELALNNTVL ETLNFYLTDI 201 AVVKIQDLEL LAKNCPNLVS VKLTDSEILD LVNFFKHASA 241 LEEFCGGTYN EEPEKYSAIS LPAKLCRLGL TYIGKNELPI 281 VFMFAAVLKK LDLLYAMLDT EDHCMLIQKC PNLEVLETRN 321 VIGDRGLEVL GRCCKRLKRL RIERGDDDQG MEDEEGTVSH 361 RGLIALSQGC SELEYM V VYV SDITNASLEH IGTHLKNLCD 401 FRLVLLDHEE KITDLPLDNG VRALLRGCNK LRRFALYLRR 441 GGLTDVGLGY IGQYSPNVRW MLLGYVGESD AGLLEFSKGC 481 PSLQKLEMRG CSFFSERALA VAATQLTSLR YLWVQGYGVS 521 PSGRDLLAMA RPFWNIELIP SRKVAMNTNS DETVVVEHPA 561 HILAYYSLAG QRSDFPDTVV PLDTATCVDT

An example of a nucleotide (cDNA) sequence that encodes the Glycine max SEQ ID NO:21 COI1 protein (NCBI cDNA accession number NM_001251661.1 (GI:351724346)) is shown below as SEQ ID NO:23.

1 ATGACGGAGG ATCGGAACGT GCGGAAGACA CGTGTGGTCG 41 ACCTGGTCCT CGACTGTGTC ATCCCTTACA TCGACGACCC 81 CAAGGACCGC GACGCCGTCT CACAGGTCTG CCGACGCTGG 121 TACGAACTCG ACTCCCTCAC TCGGAAGCAC GTCACCATCG 161 CGCTCTGCTA CACCACCACG CCGGCGCGCC TCCGCCGCCG 201 CTTCCCGCAC CTTGAGTCGC TCAAGCTCAA GGGCAAGCCC 241 CGAGCAGCAA TGTTCAACTT GATACCCGAG GATTGGGGAG 281 GCCACGTCAC CCCATGGGTC AAGGAGATTT CTCAGTACTT 321 CGATTGCCTC AAGAGTCTCC ACTTCCGCCG TATGATTGTC 361 AAAGATTCCG ATCTTCGGAA TCTCGCTCGT GACCGCGGCC 401 ACGTGCTTCA CTCTCTCAAG CTTGACAAGT GCTCCGGTTT 441 CACCACCGAT GGTCTTTTCC ATATCGGTCG CTTTTGCAAG 481 AGTTTAAGAG TCTTGTTTTT GGAGGAAAGC TCAATTGTTG 521 AGAAGGACGG AGAATGGTTA CACGAGCTTG CTTTGAATAA 561 TACAGTTCTT GAGACTCTCA ATTTTTACTT GACAGATATT 601 GCTGTTGTGA AGATTCAGGA CCTTGAACTT TTAGCTAAAA 641 ATTGCCCCAA CTTAGTGTCT GTGAAACTTA CTGACAGTGA 681 AATACTGGAT CTTGTGAACT TCTTTAAGCA TGCCTCTGCA 721 CTGGAAGAGT TTTGTGGAGG CACCTACAAT GAAGAACCAG 761 AAAAATACTC TGCTATATCA TTACCAGCAA AGTTATGTCG 801 ATTGGGTTTA ACATATATTG GAAAGAATGA GTTGCCCATA 841 GTGTTCATGT TTGCAGCCGT ACTAAAAAAA TTGGATCTCC 881 TCTATGCAAT GCTAGACACG GAGGATCATT GCATGTTAAT 921 CCAAAAGTGT CCAAATCTGG AAGTCCTTGA GACAAGGAAT 961 GTAATTGGAG ACAGAGGGTT AGAGGTTCTT GGTCGTTGTT 1001 GTAAGAGGCT AAAAAGGCTT AGGATTGAAA GGGGTGATGA 1041 TGATCAAGGA ATGGAGGATG AAGAAGGTAC TGTGTCCCAT 1081 AGAGGGCTAA TAGCCTTGTC ACAGGGCTGT TCAGAGCTTG 1121 AATACATGGC TGTTTATGTG TCTGATATTA CAAATGCATC 1161 TCTGGAACAT ATCGGAACTC ACTTGAAGAA CCTCTGCGAT 1201 TTTCGCCTTG TGTTGCTTGA CCACGAAGAG AAAATAACTG 1241 ATTTGCCACT TGACAATGGG GTGAGGGCTC TACTGAGGGG 1281 CTGTAACAAG CTGAGGAGAT TTGCTCTATA TCTCAGGCGT 1321 GGCGGGTTGA CCGATGTAGG TCTTGGTTAC ATTGGACAGT 1361 ACAGTCCAAA TGTGAGATGG ATGCTGCTTG GTTATGTGGG 1401 GGAGTCTGAT GCAGGGCTTT TGGAATTCTC TAAAGGGTGT 1441 CCTAGTCTTC AGAAACTAGA AATGAGAGGG TGTTCATTTT 1481 TCAGTGAACG TGCACTTGCT GTGGCTGCAA CACAATTGAC 1521 TTCTCTTAGG TACTTGTGGG TGCAAGGGTA TGGTGTATCT 1561 CCATCTGGAC GTGATCTTTT GGCAATGGCT CGCCCCTTTT 1601 GGAACATTGA GTTAATTCCT TCTAGAAAGG TGGCTATGAA 1641 TACCAATTCA GATGAGACGG TAGTTGTTGA GCATCCTGCT 1681 CATATTCTTG CATATTATTC TCTTGCAGGG CAGAGATCAG 1721 ATTTTCCAGA TACTGTTGTG CCTTTGGACA CTGCCACATG 1761 CGTTGACACC TAG

An example of a COI1 protein from Solanum lycopersicum (tomato) with NCBI accession number NP_001234464.1 (GI:350535701) has the following sequence (SEQ ID NO:24).

1 MEERNSTRLS SSTNDTVWEC VIPYIQESRD RDAVSLVCKR 41 WWQIDAITRK HITMALCYTA KPEQLSRRFP HLESVKLKGK 81 PRAAMFNLIP EDWGGYVTPW VMEITKSFSK LKALHFRRMI 121 VRDSDLELLA NRRGRVLQVL KLDKCSGFST DGLLHISRSC 161 KNLRTLLMEE SYIIEKDGEW AHELALNNTV LENLNFYMTD 201 LLQVRAEDLE LIARNCKSLV SMKISECEIT NLLGFFRAAA 241 ALEEFGGGAF NDQPELVVEN GYNEHSGKYA ALVFPPRLCQ 281 LGLTYLGRNE MSILFPIASR LRKLDLLYAL LDTAAHCFLL 321 QRCPNLEILE TRNVVGDRGL EVLGQYCKRL KRLRIERGAD 361 DQEMEDEEGA VTHRGLIDLA KGCLELEYM A  VYVSDITNEA 401 LEVIGTYLKN LSDFRLVLLD REERITDLPL DNGVRALLRG 441 CHNLRRFALY VRPGGLTDVG LSYVGQYSPN VRWMLLGYVG 481 ESDHGLLEFS KGCPSLQKLE VRGCCFSERA LALATLQLKS 521 LRYLWVQGYR ASSAGRDLLA MARPFWNIEL IPARRVIAND 561 GNNAETVVSE HPAHILAYYS LAGQRTDFPD TVKPLDPTYL 601 LAE

A comparison of the Arabidopsis thaliana COI1 SEQ ID NO:1 sequence and the Solanum lycopersicum COI SEQ ID NO:24 sequence is shown below, illustrating that the two proteins have at least 69% sequence identity. In addition, the location of the alanine at position 384 that can be replaced, for example with a valine, to generate a modified COI1 protein is also identified in bold and with underlining. As illustrated, this alanine is at about position 390 in the Solanum lycopersicum COI1 SEQ ID NO:24 sequence.

69.3% identity in 584 residues overlap; Score: 2071.0; Gap frequency: 1.7% Seq1 15 ATVDDVIEQVMTYITDPKDRDSASLVCRRWFKIDSETREHVTMALCYTATPDRLSRRFPN Seq24 12 STNDTVWECVIPYIQESRDRDAVSLVCKRWWQIDAITRKHITMALCYTAKPEQLSRREPH  * * * * *  **    ***  **** **  **  ** * ******** *  ****** Seq1 75 LRSLKLKGKPRAAMFNLIPENWGGYVTPWVTEISNNLRQLKSVHFRRMIVSDLDLDRLAK Seq24 72 LESVKLKGKPRAAMFNLIPEDWGGYVTPWVMEITKSFSKLKALHFRRMIVRDSDLELLAN * * **************** ********* **      **  ******* * **  ** Seq1 135 ARADDLETLKLDKCSGETTDGLLSIVTHCRKIKTLLMEESSFSEKDGKWLHELAQHNTSL Seq24 132 RRGRVLQVLKLDKCSGFSTDGLLHISRSCKNLRTLLMEESYIIEKDGEWAHELALNNTVL  *   *  ********* ***** *   *    *******   **** * ****  ** * Seq1 195 EVLNFYMTEFAKISPKDLETIARNCRSLVSVKVGDFEILELVGFFKAAANLEEFCGGSLN Seq24 192 ENLNFYMTDLLQVRAEDLELIARNCKSLVSMKISECEITNLLGFFRAAAALEEFGGGAFN * ******        *** ***** **** *    **  * *** *** **** **  * Seq1 255 E------DIGMPE---KYMNLVFPRKLCRLGLSYMGPNEMPILFPFAAQIRKLDLLYALL Seq24 252 DQPELVVENGYNEHSGKYAALVEPPRLCQLGLTYLGRNEMSILFPIASRLRKLIDLLYALL          *  *   **  ****  ** *** * * *** **** *   ********** Seq1 306 ETEDHCTLIQKCPNLEVLETPNVIGDRGLEVLAQYCKQLKRLRIERGADEQGMEDEEGLV Seq24 312 DTAAHCELLQRCPNLEILETRNVVGDRGLEVLGQYCKRLKRLRIERGADDQEMEDEEGAV  *  ** * * ***** ****** ******** **** *********** * ****** * Seq1 366 SQRGLIALAQGCQELEYM A VYVSDITNESLESIGTYLKNLCDFRLVLLDREERITDLPLD Seq24 372 THRGLIDLAKGCLELEYM A VYVSDITNEALEVIGTYLKNLSDFRLVLLDREERITDLPLD   **** ** ** *************** ** ******** ******************* Seq1 426 NGVRSLLIGCKKLRRFAFYLRQGGLTDLGLSYIGQYSPNVRWMLLGYVGESDEGLMEFSR Seq24 432 NGVRALLRGCHNLRRFALYVRPGGLTDVGLSYVGQYSPNVRWMLLGYVGESDHGLLEFSK **** ** **  ***** * * ***** **** ******************* ** *** Seq1 486 GCPNLQKLEMRGCCFSERAIAAAVTKLPSLRYLWVQGYRASMTGQDLMQMARPYWNIELI Seq24 492 GCPSLQKLEVRGCCFSERALALATLQLKSLRYLWVQGYRASSAGRDLLAMARPFWNIELI *** ***** ********* * *   * *************  * **  **** ****** Seq1 546 PSRRV-PEVNQQGEIREMEHPAHILAYYSLAGQRTDCPTTVRVL Seq24 552 PARRVIANDGNNAETVVSEHPAHILAYYSLAGQRTDFPDTVKPL * ***        *    ****************** * **  *

An example of a modified COI1 Solanum lycopersicum (tomato) protein with a valine alanine at about position 390 has the following sequence (SEQ ID NO:25).

1 MEERNSTRLS SSTNDTVWEC VIPYIQESRD RDAVSLVCKR 41 WWQIDAITRK HITMALCYTA KPEQLSRRFP HLESVKLKGK 81 PRAAMFNLIP EDWGGYVTPW VMEITKSFSK LKALHFRRMI 121 VRDSDLELLA NRRGRVLQVL KLDKCSGFST DGLLHISRSC 161 KNLRTLLMEE SYIIEKDGEW AHELALNNTV LENLNFYMTD 201 LLQVRAEDLE LIARNCKSLV SMKISECEIT NLLGFFRAAA 241 ALEEFGGGAF NDQPELVVEN GYNEHSGKYA ALVFPPRLCQ 281 LGLTYLGRNE MSILFPIASR LRKLDLLYAL LDTAAHCFLL 321 QRCPNLEILE TRNVVGDRGL EVLGQYCKRL KRLRIERGAD 361 DQEMEDEEGA VTHRGLIDLA KGCLELEYM V  VYVSDITNEA 401 LEVIGTYLKN LSDFRLVLLD REERITDLPL DKGVRALLRG 441 CHNLRRFALY VRPGGLTDVG LSYVGQYSPN VRWMLLGYVG 481 ESDHGLLEFS KGCPSLQKLE VRGCCFSERA LALATLQLKS 521 LRYLWVQGYR ASSAGRDLLA MARPFWNIEL IPARRVIAND 561 GNNAETVVSE HPAHILAYYS LAGQRTDFPD TVKPLDPTYL 601 LAE

An example of a nucleotide (cDNA) sequence that encodes the Solanum lycopersicum SEQ ID NO:24 COI1 protein (with NCBI cDNA accession number NM_001247535.1 (GI:350535700)) is shown below as SEQ ID NO:26.

1 CTCTCCTCCA TCTTCTTCAA CTGTAACCTC TCTTCCATTA 41 TCAGTGTCAA GTTGTTGAAG TTTTGGTCAT GGTCATGGTG 81 TAATTTGTTG TTAGTATTTT GAAGTATTTG TGTTTTTGAT 121 TTGGTTTTGG TTTTAATGGA GGAACGGAAC TCAACGAGAT 161 TGAGTAGCTC AACAAACGAT ACAGTATGGG AGTGTGTGAT 201 TCCGTATATA CAGGAATCGC GTGATAGAGA CGCGGTATCG 241 TTGGTATGTA AGAGGTGGTG GCAGATCGAT GCGATTACTA 281 GAAAGCATAT AACTATGGCG TTGTGTTATA CAGCGAAACC 321 AGAGCAGTTA TCTAGAAGGT TTCCACATCT TGAATCGGTT 361 AAACTGAAAG GGAAACCAAG AGCTGCTATG TTTAATTTGA 401 TACCGGAAGA TTGGGGAGGA TATGTTACAC CTTGGGTTAT 441 GGAGATAACT AAGTCGTTTA GTAAATTGAA AGCACTTCAT 481 TTTCGTAGAA TGATTGTTAG AGATTCGGAT CTCGAATTAC 521 TTGCGAATCG TCGTGGAAGA GTTCTTCAAG TTTTGAAGCT 561 GGATAAGTGT TCTGGATTTT CTACTGATGG TCTTCTGCAT 601 ATTTCTCGTT CCTGCAAGAA CTTAAGAACT TTGTTAATGG 641 AAGAGAGTTA TATAATTGAG AAAGATGGAG AATGGGCACA 681 TGAACTAGCA TTGAACAACA CTGTTCTTGA GAATTTGAAC 721 TTTTACATGA CAGATCTTCT GCAAGTTAGG GCTGAAGATC 761 TTGAATTGAT AGCAAGAAAT TGTAAATCTC TAGTCTCTAT 801 GAAAATTAGC GAGTGTGAAA TTACGAATCT TCTTGGCTTC 841 TTTAGAGCTG CGGCTGCATT GGAGGAGTTT GGTGGTGGCG 881 CATTTAATGA CCAACCAGAA CTTGTTGTTG AAAATGGCTA 921 TAATGAGCAT TCCGGAAAAT ATGCCGCACT AGTCTTCCCT 961 CCAAGATTAT GTCAATTGGG CTTGACATAC TTAGGGAGAA 1001 ATGAGATGTC CATTCTCTTT CCTATTGCGT CTCGTCTGAG 1041 GAAATTGGAT CTTCTTTATG CACTTCTTGA CACAGCAGCC 1081 CACTGTTTCT TACTGCAAAG GTGTCCCAAC TTGGAAATTC 1121 TTGAGACTAG GAATGTTGTT GGGGATAGAG GATTGGAAGT 1161 GCTTGGCCAG TACTGTAAGA GGTTAAAGCG GCTCAGGATT 1201 GAGAGAGGAG CTGATGATCA GGAGATGGAG GATGAAGAAG 1241 GTGCGGTTAC ACACAGAGGA TTGATTGATT TGGGAAAGGG 1281 ATGTCTTGAA CTAGAATACA TGGCTGTTTA TGTGTCAGAT 1321 ATTACTAATG AAGCTTTGGA AGTTATTGGT ACATATCTGA 1361 AAAATCTGAG TGATTTTCGG CTGGTTTTGC TTGACAGAGA 1401 AGAAAGAATA ACAGATCTGC CACTTGATAA TGGTGTGCGT 1441 GCTTTACTAA GAGGTTGCCA TAATCTTAGA AGATTTGCCC 1481 TCTATGTCCG GCCTGGGGGC CTTACTGATG TAGGTCTCAG 1521 TTATGTCGGG CAATACAGCC CAAACGTGAG ATGGATGCTT 1561 CTGGGATACG TTGGGGAATC CGATCATGGC CTTCTGGAGT 1601 TCTCTAAAGG ATGTCCGAGC CTGCAAAAGC TAGAAGTGAG 1641 AGGCTGCTGT TTCAGTGAAC GTGCATTAGC CTTGGCTACC 1681 TTGCAGCTAA AATCGTTAAG GTATCTATGG GTACAAGGAT 1721 ACAGGGCATC TTCAGCTGGT CGTGATCTCT TAGCGATGGC 1761 TCGCCCATTC TGGAATATTG AATTGATTCC TGCAAGACGA 1801 GTTATTGCCA ACGATGGAAA TAATGCAGAA ACTGTAGTCT 1841 CGGAGCATCC AGCCCATATA CTTGCCTACT ATTCTCTTGC 1861 CGGACAAAGA ACAGATTTTC CAGACACTGT CAAGCCTTTG 1921 GACCCAACTT ACCTTCTCGC TGAATAGGTT TGTAAATATA 1961 ACTTTTCCTT GAGTGAAGTT GTTCGAGGTC TATTTGCTTC 2001 CTTTTTAGGT GTCTTGTCCA TATGTATGCC

An example of a COI1 protein from Zea mays (corn) with NCBI accession number NP_001150429.1 (GI:226503785) has the following sequence (SEQ ID NO:27).

1 MGGEAPEPRR LTRALSIGGG DGGWVPEEML QLVMGFVEDP 41 RDREAASLVC HRWHRVDALS RKHVTVPFCY AVSPARLLAR 81 FPRLESLAVK GKPRAAMYGL IPDDWGAYAR PWITELAAPL 121 ECLKALHLRR MVVTDDDLAE LVRARGHMLQ ELKLDKCTGF 161 STHGLRLVAR SCRSLRTLFL EECQIDDKGS EWIHDLAVCC 201 PVLTTLNFHM TELEVMPADL KLLAKSCKSL ISLKISDCDL 241 SDLIEFFQFA TALEEFAGGT FNEQGELSKY VNVKFPSRLC 281 SLGLTYMGTN EMPIMFPFSA ILKKLDLQYT FLTTEDHCQL 321 IAKCPNLLVL AVRNVIGDRG LGVVADTCKK LQRLRIERGD 361 DEGGVQEEQG GVSQVGLTAI AVGCRELEYI A AYVSDITNG 401 ALESIGTFCK KLYDFRLVLL DREERITDLP LDNGVRALLR 441 GCTKLRRFAL YLRPGGLSDA GLGYIGQCSG NIQYMLLGNV 481 GETDDGLISF ALGCVNLRKL ELRSCCFSER ALALAILHMP 521 SLRYVWVQGY KASQTGRDLM LMARPFWNIE FTPPNPKNGG 561 WLMEDGEPCV DSHAQILAYH SLAGKRLDCP QSVVPLYPA

A comparison of the Arabidopsis thaliana COI1 SEQ ID NO:1 sequence and the Zea mays COI1 SEQ ID NO:27 sequence is shown below, illustrating that the two proteins have at least 58% sequence identity. In addition, the location of the alanine at position 384 that can be replaced, for example with a valine, to generate a modified COI1 protein is also identified in bold and with underlining. As illustrated, this alanine is at about position 391 in the Zea mays COI1 SEQ ID NO:27 sequence.

57.9% identity in 570 residues overlap; Score: 1722.0; Gap frequency: 0.9% Seq1 18 DDVIEQVMTYITDPKDRDSASLVCRRWFKIDSETREHVTMALCYTATPDRLSRRFPNLRS Seq27 27 EEMLQLVMGFVEDPRDPEAASLVCHRWHRVDALSRKHVTVPFCYAVSPARLLARFPPLES       **    ** ** ***** **   *   * ***   **   * **  *** * * Seq1 78 LKLKGKPRAAMFNLIPENWGGYVTPWVTEISNNLRQLKSVHFRRMIVSDLDLDRLAKARA Seq27 87 LAVKGKPRAAMYGLIPDDWGAYARPWITELAAPLECLKALHLRRMVVTDDDLAELVRARG *  ********  ***  ** *  ** **    *  **  * *** * * **  *  ** Seq1 138 DDLETLKLDKCSGFTTDGLLSIVTHCRKIKTLLMEESSFSEKDGKWLHELAQHNTSLEVL Seq27 147 HMLQELKLDKCTGFSTHGLRLVARSCRSLRTLFLEECQIDDKGSEWIHDLAVCCPVLTTL   *  ****** ** * **      **   **  **     *   * * **     *  * Seq1 198 NFYMTEFAKISPKDLETIARNCRSLVSVKVGDFEILELVGFFKAAANLEEFCGGSLNEDI Seq27 207 NFHMTEL-EVMPADLKLLAKSCKSLISLKISDCDLSDLIEFFQFATALEEFAGGTFNEQ- ** ***     * **   *  * ** * *  *     *  **  *  **** **  ** Seq1 258 GMPEKYMNLVFPRKLCRLGLSYMGPNEMPILFPFAAQIRKLDLLYALLETEDHCTLIQKC Seq27 265 GELSKYVNVKFPSRLCSLGLTYMGTNEMPIMFPFSAILKKLDLQYTFLTTEDHCQLIAKC *   ** *  **  ** *** *** ***** *** *   **** *  * ***** ** ** Seq1 318 PNLEVLETRNVIGDRGLEVLAQYCKQLKRLRIERGADEQGMEDEEGLVSQRGLIALAQGC Seq27 325 PNLLVLAVPNVIGDRGLGVVADTCKKLQRLRIERGDDEGGVQEEQGGVSQVGLTAIAVGC *** **  ********* * *  ** * ******* ** *   * * *** ** * * ** Seq1 378 QELEYMAVYVSDITNESLESIGTYLKNLCDFRLVLLDREERITDLPLDNGVRSLLIGCKK Seq27 385 RELEYIAAYVSDITNGALESIGTFCKKLYDFRLVLLDREERITDLPLDNGVRALLRGCTK  **** * *******  ******  * * *********************** ** ** * Seq1 438 LRRFAFYLRQGGLTDLGLSYIGQYSPNVRWMLLGYVGESDEGLMEFSRGCPNLQKLEMRG Seq27 445 LRRFALYLRPGGLSDAGLGYIGQCSGNIQYMLLGNVGETDDGLISFALGCVNLRKLELRS ***** *** *** * ** **** * *   **** *** * **  *  ** ** *** * Seq1 498 CCFSERAIAAAVTKLPSLRYLWVQGYRASMTGQDLMQMARPYWNIELIPS--RRVPEVNQ Seq27 505 CCFSERALALAILHMPSLRYVWVQGYKASQTGRDLMLMARPFWNIEFTPPNPKNGGWLME ******* * *    ***** ***** ** ** *** **** ****  * Seq1 556 QGEIREMEHPAHILAYYSLAGQRTDCPTTV Seq27 565 DGEPCVDSH-AQILAYHSLAGKRLDCPQSV  **     * * **** **** * ***  *

An example of a modified COI1 Zea mays (corn) protein with a valine instead of an alanine at position 391 has the following sequence (SEQ ID NO:28).

1 MGGEAPEPRR LTRALSIGGG DGGWVPEEML QLVMGFVEDP 41 RDREAASLVC HRWHRVDALS RKHVTVPFCY AVSPARLLAR 81 FPRLESLAVK GKPRAAMYGL IPDDWGAYAR PWITELAAPL 121 ECLKALHLRR MVVTDDDLAE LVRARGHMLQ ELKLDKCTGF 161 STHGLRLVAR SCRSLRTLFL EECQIDDKGS EWIHDLAVCC 201 PVLTTLNFHM TELEVMPADL KLLAKSCKSL ISLKISDCDL 241 SDLIEFFQFA TALEEFAGGT FNEQGELSKY VNVKFPSRLC 281 SLGLTYMGTN EMPIMFPFSA ILKKLDLQYT FLTTEDHCQL 321 IAKCPNLLVL AVRNVIGDRG LGVVADTCKK LQRLRIERGD 361 DEGGVQEEQG GVSQVGLTAI AVGCRELEYI V AYVSDITNG 401 ALESIGTFCK KLYDFRLVLL DREERITDLP LDNGVRALLR 441 GCTKLRRFAL YLRPGGLSDA GLGYIGQCSG NIQYMLLGNV 481 GETDDGLISF ALGCVNLRKL ELRSCCFSER ALALAILHMP 521 SLRYVWVQGY KASQTGRDLM LMARPFWNIE FTPPNPKNGG 561 WLMEDGEPCV DSHAQILAYH SLAGKRLDCP QSVVPLYPA

An example of a nucleotide (cDNA) sequence that encodes the Zea mays SEQ ID NO:27 COI1 protein (with NCBI cDNA accession number NM_001156957.1 (GI:226503784)) is shown below as SEQ ID NO:29.

1 ACCCCTGCTT GCTGCAGCTT CAAGCACTAC CGAATCAGGG 41 CGAGTGGGAG CAGAGGAGGG AATCCCATGT CTCCGCCCCT 81 CGCTGGAGCA GATCGTTGTC GAGCCGACGT GGAGCTGCTG 121 CGGTAGAAAG CTAGCGGAGC CTGCGAGCTA GCCTGATCCG 161 TCCGCAGTCC GATCGGGATC GATGGGTGGG GAGGCGCCGG 201 AGCCGCGGCG GCTGACCCGG GCGCTGAGCA TCGGCGGCGG 241 TGACGGCGGC TGGGTTCCCG AGGAGATGCT GCAACTCGTG 281 ATGGGGTTCG TCGAGGACCC GCGCGACCGG GAGGCCGCGT 321 CGCTGGTGTG TCACCGGTGG CACCGCGTCG ACGCGCTCTC 361 GCGGAAGCAC GTGACGGTGC CCTTCTGCTA CGCCGTTTCC 401 CCGGCACGCC TGCTCGCGCG GTTCCCGCGG CTCGAGTCGC 441 TCGCGGTGAA GGGGAAGCCC CGCGCGGCCA TGTACGGGCT 481 CATACCCGAC GACTGGGGCG CCTACGCCCG CCCGTGGATC 521 ACCGAGCTCG CCGCGCCGCT CGAGTGCCTC AAGGCGCTCC 561 ACCTCCGACG CATGGTCGTC ACAGACGACG ACCTCGCCGA 601 GCTCGTCCGT GCCAGGGGGC ACATGCTGCA GGAGCTGAAG 641 CTCGATAAGT GCACCGGCTT CTCCACTCAT GGACTCCGCC 681 TCGTTGCCCG CTCCTGCAGA TCACTGAGGA CTTTATTTTT 721 GGAAGAATGT CAAATTGATG ATAAGGGCAG TGAATGGATC 761 CACGATCTCG CAGTCTGCTG TCCTGTTCTG ACAACATTGA 801 ATTTCCACAT GACTGAGCTT GAAGTGATGC CAGCTGACCT 841 AAAGCTTCTT GCAAAGAGCT GCAAGTCACT GATTTCATTG 881 AAGATTAGTG ACTGCGATCT TTCAGATTTG ATAGAGTTCT 921 TCCAATTTGC CACAGCACTG GAAGAATTTG CTGGAGGGAC 961 ATTCAATGAG CAAGGGGAAC TCAGCAAGTA TGTGAATGTT 1001 AAATTTCCAT CAAGACTATG CTCCTTGGGA CTTACTTACA 1041 TGGGAACAAA TGAAATGCCC ATTATGTTCC CTTTTTCTGC 1081 AATACTAAAG AAGCTGGATT TGCAATACAC TTTCCTCACC 1121 ACTGAGGACC ATTGCCAGCT CATTGCAAAA TGCCCGAACT 1161 TACTAGTTCT CGCGGTGAGG AATGTGATTG GAGATAGAGG 1201 ATTAGGAGTT GTTGCGGATA CGTGCAAGAA GCTCCAAAGG 1241 CTCAGAATAG AGCGAGGAGA TGATGAAGGA GGTGTGCAAG 1281 AAGAGCAGGG AGGGGTCTCT CAAGTGGGCT TGACGGCTAT 1321 AGCCGTAGGT TGCCGTGAGC TGGAATATAT AGCTGCCTAT 1361 GTGTCTGATA TAACCAATGG GGCCTTGGAA TCTATCGGGA 1401 CATTCTGCAA AAAACTATAC GACTTCCGGC TTGTTCTACT 1441 TGATAGAGAA GAGAGGATAA CAGACTTGCC ACTGGACAAT 1481 GGTGTCCGAG CTTTGTTGAG GGGCTGCACC AAGCTTCGGA 1521 GGTTTGCTCT GTACTTGAGA CCAGGAGGGC TCTCAGATGC 1561 AGGTCTCGGC TACATTGGAC AGTGCAGCGG AAACATCCAG 1601 TACATGCTTC TCGGTAATGT TGGGGAAACT GATGATGGAT 1641 TGATCAGCTT CGCATTGGGT TGCGTAAACC TGCGAAAGCT 1681 TGAACTCAGG AGTTGCTGCT TCAGCGAGCG AGCACTGGCC 1721 CTTGCAATAC TACATATGCC TTCCCTGAGG TACGTATGGG 1761 TTCAGGGCTA CAAAGCGTCT CAAACCGGCC GAGACCTCAT 1801 GCTCATGGCA AGGCCCTTCT GGAACATAGA GTTTACACCT 1841 CCCAATCCTA AGAACGGAGG TTGGCTGATG GAAGATGGGG 1881 AGCCTTGTGT AGATAGTCAC GCTCAGATAC TTGCATACCA 1921 CTCCCTCGCC GGTAAGAGGC TGGACTGCCC ACAATCCGTG 1961 GTTCCTTTGT ATCCTGCGTG AGTGTAAATA GACTAAGCTG 2001 GTGTCTTTCC TTAGCCTCCT GGTCAACAAG AATGGTGTTG 2041 ATAACTCGAT ATATGCGGTT ATTGTATGGA TCTAGATGGC 2081 TAGCTGCTAC GTACTGTAAT AAGCTACTAG TAGCTGAGAG 2121 ATGTCCTGGA ATAAGCCCTT GCTATTTTTG CCTAAAAAAA 2161 AAAAAAAAA

An example of a COI1 protein from Triticum aestivum (wheat) with NCBI accession number ADK66974.1 (GI:301318118) has the following sequence (SEQ ID NO:30).

1 MGGEVPEPRR LSRALSFGVP DEALHLVMGY VDAPRDREAA 41 SLVCRRWHRI DALTRKHVTV AFCYAADPSR LLARFPRLES 81 LALKGRPRAA MYGLISDDWG AYAAPWVARL AAPLECLKAL 121 HLRRMTVTDD DVATLIRSRG HMLQELKLDK CSGFSTDALR 161 LVARSCRSLR TLFLEECVIT DEGGEWLHEL AVNNSVLVTL 201 NFYMTELKVV PADLELLAKN CKSLLSLKIS ECDLSDLIGF 241 FEAANALQDF AGGSFNEVGE LTKYEKVKFP PRVCFLGLTF 281 MGKNEMPVIF PFSASLKKLD LQYTFLTTED HCQLISKCPN 321 LFVLEVRNVI GDRGLEVVGD TCKKLRRLRI ERGDDDPGLQ 361 EEQGGVSQLG LTAVAVGCRD LEYI A AYVSD ITNGALESIG 401 TFCKNLYDFR LVLLDRQKQV TDLPLDNGVR ALLRSCTKLR 441 RFALYLRPGG LSDIGLDYIG QYSGNIQYML LGNVGESDHG 481 LIRFAIGCTN LRKLELRSCC FSEQALSLAV LHMPSLRYIW 521 VQGYKASPAG LELLLMARRF WNIEFTPPSP EGLFRMTLEG 561 EPCVDKQAQV LAYYSLAGQR QDCPDWVTPL HPAA

A comparison of the Arabidopsis thaliana COI1 SEQ ID NO:1 sequence and the Triticum aestivum COI1 SEQ ID NO:30 sequence is shown below, illustrating that the two proteins have at least 58% sequence identity. In addition, the location of the alanine at position 384 that can be replaced, for example with a valine, to generate a modified COI1 protein is also identified in bold and with underlining. As illustrated, this alanine is at about position 385 in the Triticum aestivum COI1 SEQ ID NO:30 sequence.

57.3% identity in 572 residues overlap; Score: 1724.0; Gap frequency: 0.5% Seq1 18 DDVIEVMTYITDPKDPDSASLVCRRWFKIDSETREHVTMALCYTATPDRLSRRFPNLRS Seq30 21 DEALHLVMGYVDAPRDREAASLVCRRWHRIDALTRKHVTVAFCYAADPSRLLARFPRLES *     ** *   * **  ********  **  ** *** * ** * * **  *** * * Seq1 78 LKLKGEPRAAMFNLIPENWGGYVTPWVTEISNNLRQLKSVHFRRMIVSDLDLDRLAKARA Seq30 81 LALKGRPRAAMYGLISDDWGAYAAPWVARLAAPLECLKALHLRRMTVTDDDVATLIRSRG * *** *****  **   ** *  ***      *  **  * *** * * *   *   * Seq1 138 DDLETLKLDKCSGFTTDGLLSIVTHCRKIKTLLMEESSFSEKDGKWLHELAQHNTSLEVL Seq30 141 HMLQELKLDKCSGFSTDALRLVARSCRSLRTLFLEECVITDEGGEWLHELAMNNSVLVTL   *  ********* ** *      **   **  **       * ******  *  *  * Seq1 198 NFYMTEFAKISPKDLETIARNCRSLVSVKVGDFEILELVGFFKAAANLEEFCGGSLNEDI Seq30 201 NFYMTEL-KVVPADLELLAKNCKSLLSLKISECDLSDLIGFFEAANALLQDFAGGSFNE-V ******  *  * ***  * ** ** * *        * *** **  *  * *** ** Seq1 258 GMPEKYMNLVFPRKLCRLGLSYMGPNEMPILFPFAAQIRKLDLLYALLETEDHCTLIQKC Seq30 259 GELTKYEKVKFPPRVCFLGLTFMGKNEMPVIFPFSASLKKLDLQYTFLTTEDHCQLISKC *   **    **   * ***  ** ****  *** *   **** *  * ***** ** ** Seq1 318 PNLEVLETRNVIGDRGLEVLAQYCKQLKRLRIERGADEQGMEDEEGLVSQRGLIALAQGC Seq30 319 PNLFVLEVRNVIGDRGLEVVGDTCKKLRRLRIERGDDDPGLQEEQGGVSQLGLTAVAVGC *** *** ***********    ** * ******* *  *   * * *** ** * * ** Seq1 378 QELEYM A VYVSDITNESLESIGTYLKNLCDFRLVLLDREERITDLPLDNGVRSLLIGCKK Seq30 379 RDLEYI A AYVSDITNGALESIGTFCKNLYDFRLVLLDRQKQVTDLPLDNGVRALLRSCTK   *** * *******  ******  *** *********    ********** **  * * Seq1 438 LRRFAFYLRQGGLTDLGLSYIGQYSPNVRWMLLGYVGESDEGLMEFSRGCPNLQKLEMRG Seq30 439 LRRFALYLRPGGLSDIGLDYIGQYSGNIQYMLLGNVGESDHGLIRFAIGCTNLRKLELRS ***** *** *** * ** ****** *   **** ***** **  *  ** ** *** * Seq1 498 CCFSERAIAAAVTKLPSLRYLWVQGYRASMTGQDLMQMARPYWNIELIPSRRVPEVNQQG Seq30 499 CCFSEQALSLAVLHMPSLRYIWVQGYKASPAGLELLLMARRFWNIEFTPPSPEGLFRMTL ***** *   **   ***** ***** **  *  *  ***  ****  * Seq1 558 EIRE-MEHPAHILAYYSLAGQRTDCPTTVRVL Seq30 559 EGEPCVDKQAQVLAYYSLAGQRQDCPDWVTPL *        *  ********** ***  *  *

An example of a modified Triticum aestivum (wheat) COI1 protein with a valine instead of an alanine at position 385 has the following sequence (SEQ ID NO:31).

1 MGGEVPEPRR LSRALSFGVP DEALHLVMGY VDAPRDREAA 41 SLVCRRWHRI DALTRKHVTV AFCYAADPSR LLARFPRLES 81 LALKGRPRAA MYGLISDDWG AYAAPWVARL AAPLECLKAL 121 HLRRMTVTDD DVATLIRSRG HMLQELKLDK CSGFSTDALR 161 LVARSCRSLR TLFLEECVIT DEGGEWLHEL AVNNSVLVTL 201 NFYMTELKVV PADLELLAKN CKSLLSLKIS ECDLSDLIGF 241 FEAANALQDF AGGSFNEVGE LTKYEKVKFP PRVCFLGLTF 281 MGKNEMPVIF PFSASLKKLD LQYTFLTTED HCQLISKCPN 321 LFVLEVRNVI GDRGLEVVGD TCKKLRRLRI ERGDDDPGLQ 361 EEQGGVSQLG LTAVAVGCRD LEYI V AYVSD ITNGALESIG 401 TFCKNLYDFR LVLLDRQKQV TDLPLDNGVR ALLRSCTKLR 441 RFALYLRPGG LSDIGLDYIG QYSGNIQYML LGNVGESDHG 481 LIRFAIGCTN LRKLELRSCC FSEQALSLAV LHMPSLRYIW 521 VQGYKASPAG LELLLMARRF WNIEFTPPSP EGLFRMTLEG 561 EPCVDKQAQV LAYYSLAGQR QDCPDWVTPL HPAA

Another example of a COI1 protein from Triticum aestivum (wheat) with NCBI accession number ADK66973.1 (GI:301318116) has the following sequence (SEQ ID NO:32).

1 MGGEAPEPRR LSRALSLDGG GVPEEALHLV LGYVDDPRDR 41 EAASLACRRW HHIDALTRKH VTVPFCYAVS PARLLARFPR 81 LESLGVKGKP RAAMYGLIPD DWGAYARPWV AELAAPLECL 121 KALHLRRMVV TDDDLAALVR ARGHMLQELK LDKCSGFSTD 161 ALRLVARSCR SLRTLFLEEC TITDNGTEWL HDLAANNPVL 201 VTLNFYLTYL RVEPADLELL AKNCKSLISL KISDCDLSDL 241 IGFFQIATSL QEFAGAEISE QKYGNVKLPS KLCSFGLTFM 281 GTNEMHIIFP FSAVLKKLDL QYSFLTTEDH CQLIAKCPNL 321 LVLAVRNVIG DRGLGVVGDT CKKLQRLRVE RGEDDPGMQE 361 EEGGVSQVGL TAIAVGCREL ENI A AYVSDI TNGALESIGT 401 FCKNLHDFRL VLLDKQETIT DLPLDNGARA LLRGCTKLRR 441 FALYLRPGGL SDVGLGYIGQ HSGTIQYMLL GNVGQTDGGL 481 ISFAAGCRNL RKLELRSCCF SERALALAIR QMPSLRYVWV 521 QGYRASQTGR DLMLMARPFW NIEFTPPSTE TAGRLMEDGE 561 PCVDRQAQVL AYYSLSGKRS DYPQSVVPLY PA

A comparison of the Arabidopsis thaliana COI1 SEQ ID NO:1 sequence and the Triticum aestivum COI1 SEQ ID NO:32 sequence is shown below, illustrating that the two proteins have at least 56% sequence identity. In addition, the location of the alanine at position 384 that can be replaced, for example with a valine, to generate a modified COI1 protein is also identified in bold and with underlining. As illustrated, this alanine is at about position 384 in the Triticum aestivum COI1 SEQ ID NO:32 sequence.

56.1% identity in 569 residues overlap; Score: 1679.0; Gap frequency: 1.2% Seq1 18 DDVIEQVMTYITDPKDRDSASLVCRRWFKIDSETREHVTMALCYTATPDRLSRRFPNLRS Seq32 24 EEALHLVLGYVDDPRDREAASLACRRWHHIDALTRKHVTVPFCYAVSPARLLARFPRLES       *  *  ** **  *** ****  **  ** ***   **   * **  *** * * Seq1 78 LKLKGKPRAAMFNLIPENWGGYVTPWVTEISNNLRLKSVHFRRMIVSDLDLDRLAKARA Seq32 84 LGVKGKPRAAMYGLIPDDWGAYARPWVAELAAPLECLKALHLRRMVVTDDDLAALVRARG *  ********  ***  ** *  *** *    *  **  * *** * * **  *  ** Seq1 138 DDLETLKLDKCSGFTTDGLLSIVTHCRKIKTLLMEESSFSEKDGKWLHELAQHNTSLEVL Seq32 144 HMLQLKLDKCSGFSTDALRLVARSCRSLRTLFLEECTITDNGTEWLHDLAANNPVLVTL   *  ********* ** *      **   **  **         *** **  *  *  * Seq1 198 NFYMTEFAKISPKIDLETIARNCRSLVSVKVGDFEILELVGFFKAAANLEEFCGGSLNEDI Seq32 204 NFYLT-YLRVEPADLELLAKNCKSLISLKISDCDLSDLIGFFQIATSLQFAGAEISE-- *** *      * ***  * ** ** * *  *     * ***  *  * ** *    * Seq1 258 GMPEKYMNLVFPPKLCRLGLSYMGPNEMPILFPFAAQIRKLDLLYALLETEDHCTLIQKC Seq32 261 ---QKYGNVKLPSKLCSFGLTFMGTNEMHIIFPFSAVLKKLIDLQSFLTTEDHCQLIAKC     ** *   * ***  **  ** *** * *** *   **** *  * ***** ** ** Seq1 318 PNLEVLETRNVIGDRGLEVIAQYCKQLKRLRIERGADEQGMEDEEGLVSQRGLIALAQGC Seq32 318 PNLLVLAVPNVIGDRGLGVVGDTCKKLQRLRVERGEDDPGMQEEGGVSQVGLTAIAVGC *** **  ********* *    ** * *** *** *  **  *** *** ** * * ** Seq1 378 QELEYM A VYVSDITNESLESIGTYLKNLCDFRLVLLDREERITDLPLDNGVRSLLIGCKK Seq32 378 RELENI A AYVSDITNGALESIGTFCKNLHDFRLVLLDKQETITDLPLIDNGARALLRGCTK  ***  * *******  ******  *** ********  * ********* * ** ** * Seq1 438 LRRFAFYLKGGLTDLGLSYIGQYSPNVRWMLLGYVGESDEGLMEFSRGCPNLQKLEMRG Seq32 438 LRRFALYLRPGGLSDVGLGYIGQHSGTIQYMLLGNVGQTDGGLISFAAGCRNLRKLELRS ***** *** *** * ** **** *     **** **  * **  *  ** ** *** * Seq1 498 CCFSERAIAAAVTKLPSLRYLWVQGYRASMTGQDLMQMARPYWNIELIP-SRRVPEVNQQ Seq32 498 CCFSERALALAIRQMPSLRYVWVQGYRASQTGRDLMLMARPFWNIEFTPPSTETAGRLME ******* * *    ***** ******** ** *** **** ****  * * Seq1 557 GEIREMEHPAHILAYYSLAGQRTDCPTTV Seq32 558 DGEPCVDRQAQVLAYYSLSGKRSDYPQSV          *  ****** * * * *  *

A modified COI1 Triticum aestivum (wheat) protein with a valine instead of an alanine has the following sequence (SEQ ID NO:33).

1 MGGEAPEPRR LSRALSLDGG GVPEEALHLV LGYVDDPRDR 41 EAASLACRRW HHIDALTRKH VTVPFCYAVS PARLLARFPR 81 LESLGVKGKP RAAMYGLIPD DWGAYARPWV AELAAPLECL 121 KALHLRRMVV TDDDLAALVR ARGHMLQELK LDKCSGFSTD 161 ALRLVARSCR SLRTLFLEEC TITDNGTEWL HDLAANNPVL 201 VTLNFYLTYL RVEPADLELL AKNCKSLISL KISDCDLSDL 241 IGFFQIATSL QEFAGAEISE QKYGNVKLPS KLCSFGLTFM 281 GTNEMHIIFP FSAVLKKLDL QYSFLTTEDH CQLIAKCPNL 321 LVLAVRNVIG DRGLGVVGDT CKKLQRLRVE RGEDDPGMQE 361 EEGGVSQVGL TAIAVGCREL ENI V AYVSDI TNGALESIGT 401 FCKNLHDFRL VLLDKQETIT DLPLDNGARA LLRGCTKLRR 441 FALYLRPGGL SDVGLGYIGQ HSGTIQYMLL GNVGQTDGGL 481 ISFAAGCRNL RKLELRSCCF SERALALAIR QMPSLRYVWV 521 QGYRASQTGR DLMLMARPFW NIEFTPPSTE TAGRLMEDGE 561 PCVDRQAQVL AYYSLSGKRS DYPQSVVPLY PA

An example of a nucleotide (cDNA) sequence that encodes the Triticum aestivum SEQ ID NO:32 COI1 protein (NCBI cDNA accession number HM447645.1 (GI:301318115)) is shown below as SEQ ID NO:34.

1 ACGAGCACCA CCATCGGAGA AGGGCCAGCG GGAAGGGGGG 41 AAATCAATCC CCATGCCCCC ACCCCTCGCC GGACCAGATC 81 CCCGGCGGGC CGGCGCGGAG CCTTAGGCGG GGATGGGCGG 121 GGAGGCCCCG GAGCCGCGGC GGCTGAGCCG CGCGCTCAGC 161 CTGGACGGCG GCGGCGTCCC GGAGGAGGCG CTGCACCTGG 201 TGCTCGGCTA CGTGGACGAC CCGCGCGACC GCGAGGCGGC 241 CTCGCTGGCG TGCCGCCGCT GGCACCACAT CGACGCGCTC 281 ACGCGGAAGC ACGTCACCGT GCCCTTCTGC TACGCCGTGT 321 CCCCGGCGCG CCTGCTCGCG CGCTTCCCGC GCCTCGAGTC 361 GCTCGGGGTC AAGGGCAAGC CCCGCGCCGC CATGTACGGC 401 CTCATCCCCG ACGACTGGGG CGCCTACGCC CGGCCCTGGG 441 TCGCCGAGCT CGCCGCCCCG CTCGAGTGCC TCAAGGCGCT 481 CCACCTGCGC CGCATGGTCG TCACCGACGA CGACCTCGCC 521 GCCCTCGTCC GCGCCCGCGG CCACATGCTG CAGGAGCTCA 561 AGCTCGACAA GTGCTCCGGC TTCTCCACCG ACGCCCTCCG 601 CCTCGTCGCC CGCTCCTGCA GATCACTGAG AACTTTGTTT 641 CTGGAAGAAT GTACAATTAC TGATAATGGC ACTGAATGGC 681 TCCATGACCT TGCTGCCAAC AATCCTGTTC TGGTGACCTT 721 GAACTTCTAC TTGACTTACC TCAGAGTGGA GCCAGCTGAC 761 CTCGAGCTTC TCGCCAAGAA TTGCAAGTCA CTAATTTCGT 801 TGAAGATTAG CGACTGCGAC CTTTCAGATT TGATTGGATT 841 TTTCCAAATA GCTACATCTT TGCAAGAATT TGCTGGAGCG 881 GAAATCAGTG AGCAAAAGTA TGGAAATGTT AAGCTTCCTT 921 CAAAGCTTTG CTCCTTCGGA CTTACCTTCA TGGGGACAAA 961 TGAGATGCAC ATAATCTTTC CTTTTTCTGC TGTACTCAAG 1001 AAGCTGGATT TGCAGTACAG TTTTCTCACC ACTGAAGATC 1041 ATTGCCAGCT CATTGCAAAA TGTCCAAACT TACTAGTCCT 1081 TGCGGTGAGG AATGTGATTG GGGATAGAGG ACTGGGGGTT 1121 GTCGGAGACA CATGCAAGAA GCTACAAAGG CTCAGAGTTG 1161 AGCGAGGGGA AGATGACCCT GGCATGCAAG AAGAGGAAGG 1201 CGGAGTTTCT CAAGTAGGCC TAACAGCCAT AGCCGTAGGT 1241 TGCCGTGAAC TGGAAAACAT AGCTGCCTAT GTGTCTGATA 1281 TCACAAATGG GGCCCTGGAA TCCATCGGAA CGTTCTGCAA 1321 AAATCTCCAT GACTTTCGCC TTGTCCTGCT TGACAAACAA 1361 GAGACGATAA CAGATTTGCC GCTGGACAAC GGTGCCCGCG 1401 CGCTGCTCAG GGGCTGCACC AAGCTTCGGA GGTTCGCTCT 1441 ATACCTGAGA CCAGGGGGGC TTTCAGATGT AGGCCTCGGC 1481 TACATCGGGC AGCACAGTGG AACCATCCAG TACATGCTTC 1521 TGGGTAACGT CGGGCAGACG GATGGTGGAT TGATCAGTTT 1561 CGCAGCCGGG TGCCGGAACC TGCGGAAGCT TGAACTGAGG 1601 AGCTGTTGCT TCAGCGAGCG GGCTCTGGCC CTCGCCATAC 1641 GGCAAATGCC TTCCCTGAGG TATGTGTGGG TGCAGGGCTA 1681 CAGGGCCTCT CAGACCGGCC GCGACCTCAT GCTCATGGCG 1721 CGGCCCTTCT GGAACATCGA GTTTACGCCT CCCAGCACGG 1761 AGACCGCGGG CCGGCTGATG GAAGATGGGG AGCCCTGCGT 1801 TGATAGGCAA GCTCAGGTGC TGGCGTACTA CTCCCTTTCT 1841 GGGAAGAGGT CCGACTACCC GCAGTCTGTT GTTCCTCTGT 1881 ATCCTGCGTG ACTGTAAATA CATTAAGCCG GTATGGTGTC 1921 TCTCTGGGAC GGCCCCTGGC TGGCCCTCTG CGCTTCTCGG 1961 GCAATAAGGA TGTTTGTATG TGGGTATTGT ATGGATCTGG 2001 TAGATTTTCT AGCTGCTGTG TACTGGAATA AGCGCATTGG 2041 TATTTTTGCC TGGTACTCCT ATCTAATCTT AGGAAGATGT 2081 ATACTAAAGT AACATTGTGC GAGTGAACTG TGACACTATT 2121 GCGCTTGCTT CGCAGGCATA AGCTTGTCTG GTTTCCGCGG 2161 CCTGCCC

An example of a COI1 protein from Populus trichocarpa (black cottonwood, western balsam-poplar or California poplar) with NCBI accession number XP_002312140.1 (GI:224101095) has the following sequence (SEQ ID NO:35).

1 MPYINDPRDR DAVSLVCRRW YELDALTRKN VTIAFCYSTS 41 PDRLRRRFND IESLKLKGKP RAAMFFNLIP EDWGGFVTPW 81 VNEIAESFNC LKSLHFRRMI VKDSDLELLA RSRGRLLQVL 121 KLDKCSGFST DGLSHIGRSC RQLRTLFLEE SAIVERDGDW 161 LHELATNNTV LETLNFYMTE LTRVRSEDLF LLARNCRSLV 201 SVKVSDCEIL DLVGFFHAAS ALEEFCGGSF NEPDEPDKYS 241 AVKFPPKLCC LGLSYMEKNV MSIVFPFASL LKKLDLLYAF 281 LGTEDHCVLV QRCPNLEVLE TRNVIGDRGL EALAQSCKLL 321 KRLRIERGAD EQGMEDVDGR VSHRGLIALA QGCLELEYI A 361 VYVSDITNAA LEHMGTYSKN LNDFRLVLLE QEERITDLPL 401 DNGVRALLRG CEKLQRFGLY LRPGGLTDVG LGYIGQYSRR 441 VRWMILGSVG ESDEGLLAFS RGCPSLQKLE MRACCFSESA 481 LARAALQLTS LRYLWVHGYR ETSTGHRDLL TMVRPFWNIE 521 LIPSRKVESV NEAGENIVSE NPAHILAYYS LAGPRTDFPD 561 TVRPLDPANI VAA

A comparison of the Arabidopsis thaliana COI1 SEQ ID NO:1 sequence and the Populus trichocarpa COI1 SEQ ID NO:35 sequence is shown below, illustrating that the two proteins have at least 70% sequence identity. In addition, the location of the alanine at position 384 that can be replaced, for example with a valine, to generate a modified COI1 protein is also identified in bold and with underlining. As illustrated, this alanine is at about position 360 in the Populus trichocarpa COI1 SEQ ID NO:35 sequence.

70.0% identity in 566 residues overlap; Score: 2037.0; Gap frequency: 0.5% Seq1 25 MTYITDPKDRDSASLVCRRWFKIDSETREHVTMALCYTATPDRLSRRFPNLRSLKLKGKP Seq35 1 MPYINDPRDRDAVSLVCRRWYELDALTRKNVTIAFCYSTSPDRLRRRFNDIESLKLKGKP * ** ** ***  *******   *  **  ** * **   **** ***    ******** Seq1 85 RAAMF-NLIPENWGGYVTPWVTEISNNLRQLKSVHFRRMIVSDLDLDRLAKARADDLETL Seq35 61 RAAMFFNLIPEDWGGFVTPWVNEIAESFNCLKSLHFRRMIVKDSDLELLARSRGRLLQVL ***** ***** *** ***** **      *** ******* * **  **  *   *  * Seq1 144 KLDKCSGFTTDGLLSIVTHCRKIKTLLMEESSFSEKDGEWLHELAQHNTSLEVLNFYMTE Seq35 121 KLDKCSGFSTDGLSHIGRSCKLRTLFLEESAIVERDGDWLHELATNNTVLETLNFYMTE ******** ****  *   **   **  ***   * ** ******  ** ** ******* Seq1 204 FAKISPKDLETIARNCRSLVSVKVGDFEILELVGFFKAAANLEEFCGGSLNEDIGMPEKY Seq35 181 LTRVRSEDLELLARNCRSLVSVKVSDCEILDINGFFHAASALEEFCGGSFNEP-DEPDKY        ***  ************ * *** ***** **  ******** **    * ** Seq1 264 MNLVFPRKLCRLGLSYMGPNEMPILFPFAKIRKLDLLYALLETEDHCTLIQKCPNLEVL Seq35 240 SAVKFPPKLCCLGLSYMEKNVMSIVFPFASLLKKLDLLYAFLGTEDHCVLVQRCPNLEVL     ** *** ******  * * * ****    ******* * ***** * * ******* Seq1 324 ETRNVIGDRGLEVLAQYCKQLKRLRIERGADEQGMEDEEGLVSQRGLIALAQGCQELEYM Seq35 300 ETRNVIGDRGLEALAQSCKLLKRLRIERGADEQGMEDVDGRVSHRGLIALAQGCLELEYI ************ *** ** *****************  * ** ********** **** Seq1 384 AVYVSDITNESLESIGTYLKNLCDFRLVLLDREERITIDLPLDNGVRSLLIGCKKLRRFAF Seq35 360 AVYVSDITNAALEHMGTYSKNLNDFRLVLLEQEERITDLPLDNGVRALLRGCEKLQRFGL *********  **  *** *** *******  ************** ** ** ** ** Seq1 444 YLRQGGLTDLGLSYIGQYSPNVRWMLLGYVGESDEGLMEFSRGCPNLQKLEMRGCCFSER Seq35 420 YLRPGGLTDVGLGYIGQYSRRVRWMILGSVGESDEGLLAFSRGCPSLQKLEMRACCFSES *** ***** ** ******  **** ** ********  ****** ******* ***** Seq1 504 AIAAAVTKLPSLRYLWVQGYRASMTG-QDLMQMARPYWNIELIPSRRVPEVNQQGEIREM Seq35 480 ALARAALQLTSLRYLWVHGYRETSTGHRDLLTMVRPFWNIELIPSRKVESVNEAGENIVS * * *   * ******* ***   **  **  * ** ********* *  **  ** Seq1 563 EHPAHILAYYSLAGQRTDCPTTVRVL Seq35 540 ENPAHILAYYSLAGPRTDFPDTVRPL * ************ *** * *** *

An example of a modified Populus trichocarpa COI1 protein with a valine instead of an alanine has the following sequence (SEQ ID NO:36).

1 MPYINDPRDR DAVSLVCRRW YELDALTRKN VTIAFCYSTS 41 PDRLRRRFND IESLKLKGKP RAAMFFNLIP EDWGGFVTPW 81 VNEIAESFNC LKSLHFRRMI VKDSDLELLA RSRGRLLQVL 121 KLDKCSGFST DGLSHIGRSC RQLRTLFLEE SATVERDGDW 161 LHELATNNTV LETLNFYMTE LTRVRSEDLE LLARNCRSLV 201 SVKVSDCEIL DLVGFFHAAS ALEEFCGGSF NEPDEPDKYS 241 AVKFPPKLCC LGLSYMEKNV MSIVFPFASL LKKLDLLYAF 281 LGTEDHCVLV QRCPNLEVLE TRNVIGDRGL EALAQSCKLL 321 KRLRIERGAD EQGMEDVDGR VSHRGLIALA QGCLELEYI V 361 VYVSDITNAA LEHMGTYSKN LNDFRLVLLE QEERITDLPL 401 DNGVRALLRG CEKLQRFGLY LRPGGLTDVG LGYIGQYSRR 441 VRWMILGSVG ESDEGLLAFS RGCPSLQKLE MRACCFSESA 481 LARAALQLTS LRYLWVHGYR ETSTGHRDLL TMVRPFWNIE 521 LIPSRKVESV NEAGENIVSE NPAHILAYYS LAGPRTDFPD 561 TVRPLDPANI VAA

An example of a nucleotide (cDNA) sequence that encodes the Populus trichocarpa SEQ ID NO:35 COI1 protein (NCBI cDNA accession number XM_002312104.1 (GI:224101094)) is shown below as SEQ ID NO:37.

1 ATGCCGTACA TAAACGACCC GCGGGACCGC GACGCCGTTT 41 CGTTAGTTTG CCGGAGATGG TACGAGCTAG ATGCGTTAAC 81 ACGGAAGAAC GTGACTATAG CTTTTTGTTA CAGTACAAGT 121 CCAGATCGAT TACGACGTCG TTTTAATGAC ATTGAATCAT 161 TAAAGCTAAA AGGGAAACCC CGGGCTGCTA TGTTTTTTAA 201 TTTGATACCG GAGGATTGGG GAGGGTTTGT GACTCCATGG 241 GTTAATGAAA TAGCGGAGAG TTTTAATTGC TTGAAATCGC 281 TTCATTTTAG AAGGATGATT GTTAAAGATT CGGATCTGGA 321 GTTACTTGCT AGGTCCAGAG GGAGACTTTT GCAGGTTTTG 361 AAGCTTGATA AGTGCTCTGG GTTTTCCACG GATGGCCTTT 401 CGCACATCGG TCGCTCTTGC AGGCAATTGA GAACATTATT 441 CTTGGAAGAG AGTGCAATTG TTGAGAGAGA TGGTGACTGG 481 CTCCATGAGC TTGCTACGAA CAATACAGTT CTCGAGACTC 521 TAAATTTTTA CATGACAGAA CTTACCAGAG TCAGATCGGA 561 AGACCTTGAG CTTCTTGCCA GGAACTGTCG TTCATTAGTC 601 TCTGTAAAGG TTAGCGACTG TGAAATCTTG GATCTTGTTG 641 GTTTCTTTCA TGCTGCATCT GCTTTAGAGG AATTTTGTGG 681 AGGTTCCTTC AATGAGCCAG ATGAACCAGA CAAATACTCT 721 GCTGTCAAAT TCCCCCCAAA ATTATGCTGT TTGGGTCTTA 761 GCTATATGGA GAAGAACGTA ATGTCAATAG TGTTTCCTTT 801 TGCATCCCTG CTCAAAAAGC TGGATCTCCT CTACGCTTTT 841 CTTGGCACGG AAGATCATTG TGTTTTAGTC CAAAGGTGCC 881 CCAACTTAGA AGTTCTCGAG ACAAGAAATG TTATTGGAGA 921 TAGAGGGTTG GAAGCCCTTG CCCAGAGTTG TAAGCTACTA 961 AAGAGGCTTC GAATAGAGCG TGGTGCCGAT GAGCAGGGAA 1001 TGGAGGATGT GGATGGCCGA GTTTCACATA GAGGATTAAT 1041 TGCCTTGGCT CAAGGCTGCT TAGAACTCGA GTACATCGCC 1081 GTTTATGTTT CTGATATTAC CAATGCAGCT CTAGAACATA 1121 TGGGCACATA CTCAAAGAAC CTCAATGATT TCCGCCTGGT 1161 CTTGCTTGAG CAAGAAGAGA GGATAACCGA CCTGCCCCTT 1201 GACAATGGAG TTCGAGCTCT ATTAAGGGGC TGTGAAAAGC 1241 TCCAAAGGTT CGGTCTGTAT CTCCGACCAG GGGGTTTGAC 1281 TGATGTGGGT CTTGGATATA TTGGACAGTA CAGCAGACGA 1321 GTAAGATGGA TGATTCTAGG TAGTGTTGGG GAGTCTGATG 1361 AAGGGCTTTT GGCGTTTTCT AGAGGCTGTC CTAGCCTGCA 1401 AAAACTTGAA ATGAGGGCCT GTTGCTTCAG TGAGAGTGCA 1441 CTGGCTAGAG CTGCCTTGCA ACTGACTTCT CTGAGGTACT 1481 TGTGGGTGCA TGGTTATAGA GAGACCTCTA CTGGTCATCG 1521 TGATCTCTTA ACAATGGTTC GCCCATTTTG GAACATCGAA 1561 TTGATTCCTT CTAGGAAGGT TGAGTCGGTT AATGAAGCTG 1601 GAGAAAATAT TGTTTCCGAG AATCCAGCCC ACATTCTTGC 1641 ATATTACTCC CTTGCTGGAC CAAGAACAGA CTTTCCAGAT 1681 ACTGTGAGAC CACTGGATCC AGCGAACATA GTTGCTGCGT 1721 AGAGCTGTAT ATGAAGTTGA TGTCATGTTC TTTTTATTGC 1761 CACGCCCTGT TTATAGATTT ATCCATCTTT TTATCATTTG 1801 GGTAAGAGTG TTTCGGTTTA ATTTTAAATT TCTATTTTAC 1841 TTAGACCGTT GTCCTGTAAT AAGTCTACGT TCTCTGCTGT 1881 AATTTAGCAC TTCCGCTCTA GGTACACTAC TGTCTTTTCT 1921 GTCGTCTGTG GCAGTTAGCT TAACCTTTTG GTGACTTTGT 1961 ATTTCATCTG CTTCAATGTT GGAAATGTTG CTAGAATTTT 2001 GGCTGCTTTT TATTGATAAA TACACAGATT TTCACTTGCA

An example of a COI1 protein from Arachis hypogaeal (peanut) with NCBI accession number AGH62009.1 (GI:469609864) has the following sequence (SEQ ID NO:38).

1 RHCKKLQRLW IMDSIGDKGL GVVANTCKEL QELRVFPSDN 41 IGQHAAVTEK GLVAISMGCP KLHSL L YFCH QMTNAALITV 81 AKNCPNFIRF RLAILDATKP DPDTNQPLDE GFGAIVQSCR 121 RLRRLSLSGQ LTDKVFLYIG MYAEQLEMLS IAFAGESDKG 161 MLYVLNGCKK LRKLEIRDCP FGNTALLTDV GKYETMRSLW 201 MSSCEVTVGA CKVLAMKMPR LNVEIFNENE PADCEPDDVQ 241 KVEKMYLYRT LAGKRKDAPE YVWTL

A comparison of the Arabidopsis thaliana COI1 SEQ ID NO:1 sequence and the Arachis hypogaeal COI1 SEQ ID NO:38 sequence is shown below, illustrating that the two proteins have at least 31% sequence identity. In addition, the location of the alanine at position 384 that can be replaced, for example with a valine, to generate a modified COI1 protein is also identified in bold and with underlining. As illustrated, instead of an alanine, the Arachis hypogaeal COI1 sequence has a leucine at the equivalent position (66). Such a leucine at position 66 of the Arachis hypogaeal COI1 protein (SEQ ID NO:38) sequence can be modified and in some cases, it can be replaced with a valine.

31.0% identity in 274 residues overlap; Score: 312.0; Gap frequency: 4.7% Seq1 317 CPNLEVLETRNVIGDRGLEVLAQYCKQLKRLRIERGADEQGMEDEEGLVSQRGLIALAQG Seq38 3 CKKLQRLWIMDSIGDKGLGYVANTCKELQELRVFP-SDNIG---QHAAVTEKGLVAISMG *  *  *     *** ** * *  ** *  **     *  *       *   ** *   * Seq1 377 CQELEYMAVYVSDITNESLESIGTYLKNLCDFRLVLLD--REERITDLPLDNGVRSLLIG Seq38 59 CPKLKSLLYFCHQMTNAALITVAKNCPNFIRFRLAILDATKPDPDTNQPLDEGFGAIVQS *  *          **  *        *   ***  **       *  *** * Seq1 435 CKKLRRFAFYLRQGGLTDLGLSYIGQYSPNVRWMLLGYVGESDEGIMEFSRGCPNLQKLE Seq38 119 CRRLRRLSL---SGQLTDKVFLYIGMYAEQLEMLSIAFAGESDKGMLYVLNGCKKLRKLE *  ***       * ***    *** *            **** *      **  * *** Seq1 495 MRGCCFSERAIAAAVTKLPSLRYLWVQGYRASMTGQDLMQMARPYWNIELIPSRRVPEVN Seq38 176 IRDCPFGNTALLTDVGKYETMRSLWMSSCEVTVGACKVLAMKMPRLNVEIF-NENEPADC *  ***       * ***    *** *            **** *      **  * *** Seq1 555 QQGEIREMEHPAHILAYYSLAGQRTDCPTTVRVL Seq38 235 EPDDVQKVE---KMYLYRTLAGKRKDAPEYVWTL         *       *  *** * * *  *  *

An example of a modified Arachis hypogaeal (peanut) COI1 protein with a valine instead of a leucine has the following sequence (SEQ ID NO:39).

1 RHCKKLQRLW IMDSIGDKGL GVVANTCKEL QELRVFPSDN 41 IGQHAAVTEK GLVAISMGCP KLHSL V YFCH QMTNAALITV 81 AKNCPNFIRF RLAILDATKP DPDTNQPLDE GFGAIVQSCR 121 RLRRLSLSGQ LTDKVFLYIG MYAEQLEMLS IAFAGESDKG 161 MLYVLNGCKK LRKLEIRDCP FGNTALLTDV GKYETMRSLW 201 MSSCEVTVGA CKVLAMKMPR LNVEIFNENE PADCEPDDVQ 241 KVEKMYLYRT LAGKRKDAPE YVWTL

An example of a nucleotide (cDNA) sequence that encodes the Arachis hypogaeal SEQ ID NO:38 COI1 protein (with NCBI cDNA accession number KC355791.1 (GI:469609863)) is shown below as SEQ ID NO:40.

1 CGTCACTGCA AGAAACTTCA GCGCTTATGG ATAATGGATT 41 CCATTGGAGA TAAAGGGCTA GGTGTTGTAG CTAACACATG 81 TAAGGAATTG CAAGAATTGA GGGTTTTTCC TTCCGACAAC 121 ATTGGTCAGC ATGCGGCTGT CACAGAGAAG GGATTGGTTG 161 CGATATCTAT GGGCTGCCCG AAACTTCACT CATTGCTCTA 201 CTTCTGCCAC CAGATGACAA ATGCTGCCCT AATAACTGTG 241 GCCAAGAACT GCCCGAATTT TATCCGCTTT AGGTTGGCCA 281 TCCTTGACGC AACAAAACCC GACCCCGACA CAAATCAGCC 321 ACTGGATGAA GGTTTTGGGG CGATTGTGCA ATCTTGCAGG 361 CGTCTTAGGC GGCTTTCCCT CTCTGGCCAG CTGACTGATA 401 AGGTATTCCT CTACATCGGA ATGTATGCTG AGCAGCTTGA 441 GATGTTGTCC ATTGCCTTTG CCGGGGAGAG CGACAAGGGG 481 ATGCTCTATG TTCTGAACGG ATGCAAGAAG CTCCGCAAGC 521 TTGAGATCAG GGACTGCCCT TTCGGCAACA CGGCACTTCT 561 GACAGACGTA GGGAAGTATG AAACAATGCG ATCCCTTTGG 601 ATGTCGTCGT GCGAAGTAAC CGTCGGAGCA TGCAAGGTGC 641 TAGCAATGAA GATGCCGAGG CTAAATGTTG AGATCTTCAA 681 CGAGAATGAG CCAGCCGACT GCGAGCCGGA TGATGTGCAG 721 AAGGTGGAGA AGATGTACTT GTACCGGACA TTGGCTGGGA 761 AGAGGAAAGA TGCACCGGAA TATGTATGGA CCCTTTAGGT 801 GCATTTTTAG GTCAATTTTA ATTTTATTGT TATTATTGAG 841 CAGTTTGTAC GTTAGGCTGA CTTATTAATG CAATTTTAGC 881 CTTGTGTAGT GGTTGGTTTG

An example of a COI1 protein from Physcomitrella patens (earthmoss) with NCBI accession number XP_001776814.1 (GI:168048721) has the following sequence (SEQ ID NO:41).

1 MGREKRPSGS GTGLSDETLA CVLKYVESAE DRASVSLVCK 41 QWRLVDGATR KFVTIAYMYS TSPEMLTRRF KRLEGLKLKG 61 KPRAAEYDLL VPDWGGYAEP WIRDLGRAYT SLQTLQLRRC 121 QVSNADLTLI ASSPCQASLQ VLYLHKCAGF STAGLLPVAK 161 SCRSLKSLSV EDSDVTDEGG EWLFELARNN SVLEVLNFAV 201 LGLEDVDAAD LVLLVERCKS LVSLKVGEVE MVDMISAISR 241 ASSLTEFGTG SCNFFGDEDS RTHVSISLPS SLTGLSGLWA 281 MSDPGLAMVL PIAPNLRKLD LKFTLLSRKA YCQLFSQCHA 321 LEELQVRNAV GDEGMEVIGK TCKSLRRLRV EHDNAGAITQ 361 RGVVAVAQGC ARMQQL I VYV SDITNAALAM LGQCCAQLTD 401 FRLVLETAAR RVVDLPLDDG IKLLLKGCRK ISKLAVYLRH 441 GGLTDRGMGY IGEFGTNLKW LLLGCTGESD IGLASLAYKA 481 QRIERLECRD CPFGEAGLAA AVVAMSSLKF IWIQGYRAPW 521 AGEHLLALSR PYLNIEVISS TDTQPGQLIA HYTTVGPRTD 561 NPLEVKQLTL NPDDHLQEMR PSLHSPGSTR H

A comparison of the Arabidopsis thaliana COI1 SEQ ID NO:1 sequence and the Physcomitrella patens COI1 SEQ ID NO:41 sequence is shown below, illustrating that the two proteins have at least 40% sequence identity. In addition, the location of the alanine at position 384 that can be replaced, for example with a valine, to generate a modified COI1 protein is also identified in bold and with underlining. As illustrated, instead of an alanine, the Physcomitrella patens COI1 SEQ ID NO:41 sequence has a isoleucine at the equivalent position (377). Such an isoleucine at position 377 of the Physcomitrella patens COI1 protein (SEQ ID NO:41) sequence can be modified and in some cases, it can be replaced with a valine.

41.5% identity in 544 residues overlap; Score: 1109.0; Gap frequency: 2.0% Seq1 7 KRCKLSCVATVDDVIEQVMTYITDPKDRDSASLVCRRWFKIDSETREHVTMALCYTATPD Seq41 5 KRPSGSGTGLSDETLACVLKYVESAEDRASVSLVCKQWRLVDGATRKFVTIAYMYSTSPE **   *     *     *  *     ** * ****  *   *  **  ** *  *   * Seq1 67 RLSRRFPNLRSLKLKGKPRAAMFNLIPENWGGYVTPWVTEISNNLRQLKSVHFRRMIVSD Seq41 65 MLTRRFKRLEGLKLKGKPRAAEYDLLVPDWGGYAEPWIRDLGRAYTSLQTLQLRRCQVSN  * ***  *  **********   *    ****  **          *     **  ** Seq1 127 LDLDRLAKARAD-DLETLKLDKCSGFTTDGLLSIVTHCRKIKTLLMEESSFSEKDGKWLH Seq41 125 ADLTLIASSPCQASLQVLYLHKCAGFSTAGLLPVAKSCRSLKSLSVEDSDVTDEGGEWLF  **   *       *  * * ** ** * ***     **  * *  * *      * ** Seq1 186 ELAQHNTSLEVLNFYMTEFAKISPKDLETIARNCRSLVSVKVGDFEILELVGFFKAAANL Seq41 185 ELARNNSVLEVLNFAVLGLEDVDAADLVLLVERCKSLVSLKVGEVEMVDMISAISRASSL ***  *  ******           **      * **** ***  *          *  * Seq1 246 EEFCGGSLNEDIGMPEK-YMNLVFPRKLCRL-GLSYMGPNEMPILFPFAAQIRKLDLLYA Seq41 245 TEFGTGSCNFFGDEDSRTHVSISLPSSLTGLSGLWAMSDPGLAMVLPIAPNLRKLDLKFT  **  ** *               *  *  * **  *         * *   ***** Seq1 304 LLETEDHCTLIQKCPNLEVLETRNVIGDRGLEVLAQYCKQLKRLRIERGADEQGMEDEEG Seq41 305 LLSRKAYCQLFSQCHALEELQVRNAVGDEGMEVIGKTCKSLRRLRVEH--------DNAG **     * *   *  ** *  **  ** * **    ** * *** *         *  * Seq1 364 LVSQRGLIALAQGCQELEYM A VYVSDITNESLESIGTYLKNLCDFRLVLLDREERITDLP Seq41 357 AITQRGVVAVAQGCARMQQL I VYVSDITNAALAMLGQCCAQLTDFRLVLETAARRVVDLP    ***  * ****       ********  *   *     * ******     *  *** Seq1 424 LDNGVRSLLIGCKKLRRFAFYLRQGGLTDLGLSYIGQYSPNVRWMLLGYVGESDEGLMEF Seq41 417 LDDGIKLLLKGCRKISKLAVYLRHGGLTDRGMGYIGEFGTNLKWLLLGCTGESDIGLASL ** *   ** ** *    * *** ***** *  ***    *  * ***  **** ** Seq1 484 SRGCPNLQKLEMRGCCFSERAIAAAVTKLPSLRYLWVQGYRASMTGQDLMQMARPYWNIE Seq41 477 AYKAQRIERLECRDCPFGEAGLAAAVVAMSSLKFIWIQGYRAPWAGEHLLALSRPYLNIE          ** * * * *   ****    **   * *****   *  *    *** *** Seq1 544 LIPS Seq41 537 VISS  * *

An example of a modified COI1 Physcomitrella patens protein with a valine instead of an isoleucine at position 377 has the following sequence (SEQ ID NO:42).

1 MGREKRPSGS GTGLSDETLA CVLKYVESAE DRASVSLVCK 41 QWRLVDGATR KFVTIAYMYS TSPEMLTRRF KRLEGLKLKG 61 KPRAAEYDLL VPDWGGYAEP WIRDLGRAYT SLQTLQLRRC 121 QVSNADLTLI ASSPCQASLQ VLYLHKCAGF STAGLLPVAK 161 SCRSLKSLSV EDSDVTDEGG EWLFELARNN SVLEVLNFAV 201 LGLEDVDAAD LVLLVERCKS LVSLKVGEVE MVDMISAISR 241 ASSLTEFGTG SCNFFGDEDS RTHVSISLPS SLTGLSGLWA 281 MSDPGLAMVL PIAPNLRKLD LKFTLLSRKA YCQLFSQCHA 321 LEELQVRNAV GDEGMEVIGK TCKSLRRLRV EHDNAGAITQ 361 RGVVAVAQGC ARMQQL V VYV SDITNAALAM LGQCCAQLTD 401 FRLVLETAAR RVVDLPLDDG IKLLLKGCRK ISKLAVYLRH 441 GGLTDRGMGY IGEFGTNLKW LLLGCTGESD IGLASLAYKA 481 QRIERLECRD CPFGEAGLAA AVVAMSSLKF IWIQGYRAPW 521 AGEHLLALSR PYLNIEVISS TDTQPGQLIA HYTTVGPRTD 561 NPLEVKQLTL NPDDHLQEMR PSLHSPGSTR H

An example of a nucleotide (cDNA) sequence that encodes the Physcomitrella patens SEQ ID NO:40 COI1 protein (with NCBI cDNA accession number KC355791.1 (GI:469609863)) is shown below as SEQ ID NO:43.

1 ATGGGGCGAG AGAAGAGACC ATCAGGATCT GGGACGGGCT 41 TATCCGACGA GACCCTGGCG TGTGTGTTGA AGTATGTGGA 81 GAGTGCGGAG GATAGAGCGT CAGTCTCCCT GGTGTGCAAG 121 CAATGGCGAC TCGTGGATGG TGCCACGAGG AAGTTTGTAA 161 CGATAGCTTA CATGTACTCC ACTAGCCCTG AGATGCTCAC 201 CCGACGCTTC AAGCGCCTGG AAGGGCTTAA GCTGAAGGGG 241 AAGCCTCGCG CTGCGGAATA TGATTTACTA GTACCCGATT 281 GGGGTGGATA TGCTGAGCCC TGGATTCGGG ATCTGGGGCG 321 CGCATATACA AGTCTGCAAA CGCTGCAACT GCGTCGGTGC 361 CAGGTTTCTA ATGCGGATTT GACCTTAATT GCGTCTTCTC 401 CCTGTCAAGC GTCTCTGCAA GTTTTGTATT TACATAAATG 441 CGCTGGGTTT TCCACCGCTG GCCTCCTCCC TGTTGCTAAG 481 TCCTGCCGGT CTCTGAAGTC TTTGAGCGTA GAGGACAGCG 521 ATGTAACTGA TGAAGGTGGA GAGTGGCTAT TCGAGCTGGC 561 CCGCAACAAT TCCGTGTTGG AGGTCCTGAA TTTTGCTGTA 601 CTTGGTCTTG AGGATGTTGA TGCAGCTGAC TTGGTGTTGC 641 TAGTGGAGAG GTGCAAATCA CTGGTTTCTC TAAAAGTTGG 681 TGAAGTTGAA ATGGTGGACA TGATAAGTGC CATTAGCAGA 721 GCGTCTTCTT TGACTGAATT CGGCACAGGC TCTTGCAATT 761 TCTTCGGGGA CGAGGACAGC AGGACACATG TATCTATATC 801 TTTACCTTCA AGCTTGACGG GTTTGTCAGG TTTGTGGGCC 841 ATGTCCGACC CTGGATTGGC TATGGTTCTT CCCATAGCAC 881 CAAACTTGAG AAAACTGGAC CTGAAGTTCA CGCTTTTGAG 921 CAGAAAAGCT TACTGCCAAC TTTTCAGTCA GTGCCATGCT 961 TTGGAAGAGC TTCAGGTTCG CAACGCAGTT GGGGACGAGG 1001 GCATGGAAGT TATCGGCAAG ACATGCAAGA GCCTCAGGCG 1041 ATTACGCGTG GAGCACGATA ATGCAGGAGC TATCACTCAA 1081 CGAGGCGTTG TTGCTGTTGC CCAAGGGTGT GCACGAATGC 1121 AGCAGTTGAT CGTGTACGTG TCCGACATCA CCAACGCCGC 1161 GCTGGCGATG CTGGGACAAT GCTGCGCACA GCTGACGGAC 1201 TTCCGTCTCG TGCTGGAGAC CGCTGCAAGA CGCGTCGTCG 1241 ACCTGCCGTT GGACGATGGA ATCAAGCTCC TGCTCAAAGG 1281 CTGCCGAAAA ATATCCAAGC TTGCTGTATA TCTTCGGCAC 1321 GGGGGCTTGA CAGACAGAGG AATGGGTTAC ATCGGGGAGT 1361 TTGGCACGAA TTTGAAATGG TTATTGTTGG GATGCACAGG 1401 CGAATCCGAC ATTGGATTGG CCAGTTTGGC ATACAAAGCG 1441 CAGCGCATTG AAAGGTTAGA GTGTCGGGAT TGTCCGTTTG 1481 GGGAGGCAGG TCTTGCGGCA GCAGTAGTGG CGATGAGCTC 1521 GCTCAAGTTT ATATGGATTC AAGGCTATAG GGCTCCATGG 1561 GCAGGAGAGC ATCTACTGGC CTTATCACGA CCGTATCTGA 1601 ACATAGAAGT TATCTCCTCA ACAGACACCC AACCAGGCCA 1641 GCTCATAGCC CACTATACCA CTGTCGGGCC TCGCACTGAT 1681 AACCCTTTGG AGGTAAAGCA GCTGACGTTA AACCCGGACG 1721 ATCACCTGCA GGAAATGCGA CCGAGTTTAC ACTCACCTGG 1761 ATCTACGCGG CACTAAGCAG AGATTAGGCC AAGCGTCATT 1801 GCTTTCAGGC CCTCTATTGA TTTCTGTCTT CTAGCCGCGG 1841 ATGGTCGCAG TGCGCCGTTG GATACCCTAC CAGAAGCGTG 1881 GCTATTAATA CTAATGAGTG TTTGCCAGAA CGGCCCTTGA 1921 TTGTGGTCTG TGGTGGACGT TTACTGACAG CAGGAGGTGT 1961 ACGAGAGATT GCCCCTCATT GTAAAATCTG TATTAGGACA 2001 GCTAGGCTAC CAATGCTGCT GTTTCAAGTC CTTGAAACAG 2041 TGAAGATGTT GCATGCGTAC GAGGACTGCC TACTACTGTA 2081 TAAGTGTAGT GCAATGTGAA AGTGTAATGT AGTGTATTGA 2121 AATTGGGCAA GGAGTTATGG GAAAGGCTAT GTAGCTGACA 2161 CAGTTGAATG TACCTATTGT GCATTTTGGA GAAA

An example of a COI1 protein from Oryza sativa Japonica Group (rice) with NCBI accession number XP_015639870.1 (GI:1002271090) has the following sequence (SEQ ID NO:44).

1 MGGEAPEARR LDRAMSFGGA GSIPEEALHL VLGYVDDPRD 41 REAVSLVCRR WHRIDALTRK HVTVPFCYAA SPAHLLARFP 81 RLESLAVKGK PRAAMYGLIP EDWGAYARPW VAELAAPLEC 121 LKALHLRRMV VTDDDLAALV RARGHMLQEL KLDKCSGFST 161 DALRLVARSC RSLRTLFLEE CSIADNGTEW LHDLAVNNPV 201 LETLNFHMTE LTVVPADLEL LAKKCKSLIS LKISDCDFSD 241 LIGFFRMAAS LQEFAGGAFI EQGELTKYGN VKFPSRLCSL 281 GLTYMGTNEM PIIFPFSALL KKLDLQYTFL TTEDHCQLIA 321 KCPNLLVLAV RNVIGDRGLG VVADTCKKLQ RLRVERGDDD 361 PGLQEEQGGV SQVGLTTVAV GCRELEY I AA YVSDITNGAL 401 ESIGTFCKNL CDFRLVLLDR EERITDLPLD NGVRALLRGC 441 TKLRRFALYL RPGGLSDTGL GYIGQYSGII QYMLLGNVGE 481 TDDGLIRFAL GCENLRKLEL RSCCFSEQAL ARAIRSMPSL 521 RYVWVQGYKA SKTGHDLMLM ARPFWNIEFT PPSSENANRM 561 REDGEPCVDS QAQILAYYSL AGKRSDCPRS VVPLYPA

A comparison of the Arabidopsis thaliana COI1 SEQ ID NO:1 sequence and the Oryza saliva COI1 SEQ ID NO:44 sequence is shown below, illustrating that the two proteins have at least 59% sequence identity. In addition, the location of the alanine at position 384 that can be replaced, for example with a valine, to generate a modified COI1 protein is also identified in bold and with underlining. As illustrated, the Oryza sativa COI1 SEQ ID NO:44 sequence has an alanine at the equivalent position (389). Such an alanine at position 389 of the Oryza sativa COI1 protein (SEQ ID NO:44) sequence can be modified and in some cases, it can be replaced with a valine.

59.1% identity in 570 residues overlap; Score: 1768.0; Gap frequency: 0.9% Seq1 18 DDVIEQVMTYITDPKDRDSASLVCRRWFKIDSETREHVTMALCYTATPDRLSRRFPNLRS Seq44 25 EEALHLVLGYVDDPRDREAVSLVCRRWHRIDALTRKHVTVPFCYAASPAHLLARFPRLES       *  *  ** **   *******  **  ** ***   ** * *  *  *** * * Seq1 78 LKLKGKPRAAMFNLIPENWGGYVTPWVTEISNNLRQLKSVHFRRMIVSDLDLDRLAKARA Seq44 85 LAVKGEPRAAMYGLIPEDWGAYARPWVAELAAPLECLKALHLRRMVVTDDDLAALVRARG *  ********  **** ** *  *** *    *  **  * *** * * **  *  ** Seq1 138 DDLETLKLDKCSGFTTDGLLSIVTHCRKIKTLLMEESSFSEKDGKWLHELAQHNTSLEVL Seq44 145 HMLQELKLDKCSGFSTDALRLVARSCRSLRTLFLEECSIADNGTEWLHDLAVNNPVLETL   *  ********* ** *      **   **  ** *       *** **  *  ** * Seq1 198 NFYMTEFAKISPKDLETIARNCRSLVSVKVGDFEILELVGFFKAAANLEEFCGGSLNEDI Seq44 205 NFHMTELTVV-PADLELLAKKCKSLISLKISDCDFSDLIGFFRMAASLQEFAGGAFIEQ- ** ***     * ***  *  * ** * *  *     * ***  ** * ** **   * Seq1 258 GMPEKYMNLVFPRKLCRLGLSYMGPNEMPILFPFAAQIRKLDLLYALLETEDHCTLIQKC Seq44 263 GELTKYGNVKFPSRLCSLGLTYMGTNEMPIIFPFSALLKKLDLQYTFLTTEDHCQLIAKC *   ** *  **  ** *** *** ***** *** *   **** *  * ***** ** ** Seq1 318 PNLEVLETRNVIGDRGLEVLAQYCKQLKRLRIERGADEQGMEDEEGLVSQRGLIALAQGC Seq44 323 PNLLVLAVRNVIGDRGLGVVADTCKKLQRLRVERGDDDPGLQEEQGGVSQVGLTTVAVGC *** **  ********* * *  ** * *** *** *  *   * * *** **   * ** Seq1 378 QELEYM A VYVSDITNESLESIGTYLKNLCDFRLVLLDREERITDLPLDNGVRSLLIGCKK Seq44 383 RELEYI A AYVSDITNGALESIGTFCKNLCDFRLVLLDREERITDLPLDNGVRALLRGCTK  **** * *******  ******  *************************** ** ** * Seq1 438 LRRFAFYLRQGGLTDLGLSYIGQYSPNVRWMLLGYVGESDEGLMEFSRGCPNLQKLEMRG Seq44 443 LRRFALYLRPGGLSDTGLGYIGQYSGIIQYMLLGNVGETDDGLIRFALGCENLRKLELRS ***** *** *** * ** ******     **** *** * **  *  ** ** *** * Seq1 498 CCFSERAIAAAVTKLPSLRYLWVQGYRASMTGQDLMQMARPYWNIELIP--SRRVPEVNQ Seq44 503 CCFSEQALARAIRSMPSLRYVWVQGYKASKTGHDLMLMARPFWNIEFTPPSSENANRMRE ***** * * *    ***** ***** ** ** *** **** ****  *  * Seq1 556 QGEIREMEHPAHILAYYSLAGQRTDCPTTV Seq44 563 DGEPC-VDSQAQILAYYSLAGKRSDCPRSV  **       * ********* * ***  *

An example of a modified COI1 Oryza sativa protein with a valine instead of an alanine at position 389 has the following sequence (SEQ ID NO:45).

1 MGGEAPEARR LDRAMSFGGA GSIPEEALHL VLGYVDDPRD 41 REAVSLVCRR WHRIDALTRK HVTVPFCYAA SPAHLLARFP 81 RLESLAVKGK PRAAMYGLIP EDWGAYARPW VAELAAPLEC 121 LKALHLRRMV VTDDDLAALV RARGHMLQEL KLDKCSGFST 161 DALRLVARSC RSLRTLFLEE CSIADNGTEW LHDLAVNNPV 201 LETLNFHMTE LTVVPADLEL LAKKCKSLIS LKISDCDFSD 241 LIGFFRMAAS LQEFAGGAFI EQGELTKYGN VKFPSRLCSL 281 GLTYMGTNEM PIIFPFSALL KKLDLQYTFL TTEDHCQLIA 321 KCPNLLVLAV RNVIGDRGLG VVADTCKKLQ RLRVERGDDD 361 PGLQEEQGGV SQVGLTTVAV GCRELEYI V A YVSDITNGAL 401 ESIGTFCKNL CDFRLVLLDR EERITDLPLD NGVRALLRGC 441 TKLRRFALYL RPGGLSDTGL GYIGQYSGII QYMLLGNVGE 481 TDDGLIRFAL GCENLRKLEL RSCCFSEQAL ARAIRSMPSL 521 RYVWVQGYKA SKTGHDLMLM ARPFWNIEFT PPSSENANRM 561 REDGEPCVDS QAQILAYYSL AGKRSDCPRS VVPLYPA

An example of a nucleotide (cDNA) sequence that encodes the Oryza sativa SEQ ID NO:44 COI1 protein (with NCBI cDNA accession number XM_015784384.1 (GI:1002271089)) is shown below as SEQ ID NO:46.

1 CTGCGATTGC CATCCCGGCC ACCTCCAAAG GCTTTAGCCG 41 GCGGGGGACA AAGGGCGGCC CACCCCCTGC GTGCGCCAAG 81 CAATTTGGCC GCCTGACCCC GTGCCGACGT GGCCCGGCAT 121 CCCCTAGCTG GATCCCGCAG AAGTAAACGC CCGCCTCCTC 161 CCCCAATCCC CATCTCCTCT CCACTCTTCT TCTCCCTCCA 201 ATAATTCTCT CCCCTCTCCT CCTCTTCACC ACCACCACCA 241 CCACCAGCAG CAGCAGAGAG CACCATCTCC ATCCAATAAT 281 CCCCATGCTT GCGCACCACT CCCGGCCACA TCCCGCGCGA 321 GGAGGAGGAG GAGGAGGAGG GTGTGCTTGA TCCGCGCTCC 361 CGCCTGGTTG GTGGTGGTGG GGTGAGGGGG GAGGGATGGG 401 AGGGGAGGCA CCGGAGGCGC GGCGGTTGGA CCGCGCGATG 441 AGCTTCGGCG GCGCGGGCAG CATCCCGGAG GAGGCGCTGC 481 ACCTGGTGCT GGGGTACGTG GACGACCCGC GGGACAGGGA 521 GGCGGTGTCG CTCGTGTGCC GCCGCTGGCA CCGCATCGAC 561 GCGCTCACGC GGAAGCACGT CACCGTGCCC TTCTGCTACG 601 CCGCGTCGCC CGCGCACCTG CTCGCGCGGT TCCCGCGGCT 641 GGAGTCGCTC GCGGTCAAGG GGAAGCCGCG CGCCGCCATG 681 TACGGGCTCA TCCCGGAGGA CTGGGGCGCC TACGCGCGCC 721 CCTGGGTCGC CGAGCTCGCC GCGCCGCTCG AGTGCCTCAA 761 GGCGCTCCAC CTGCGCCGCA TGGTCGTCAC CGACGACGAC 801 CTCGCCGCGC TCGTCCGCGC CCGCGGCCAC ATGCTGCAGG 841 AGCTCAAGCT CGACAAGTGC TCCGGCTTCT CCACCGACGC 881 TCTCCGCCTC GTCGCCCGCT CCTGCAGATC ACTGAGAACA 921 TTATTTCTGG AGGAATGCTC AATTGCTGAT AATGGTACTG 961 AATGGCTCCA CGACCTTGCT GTCAACAATC CTGTTCTGGA 1001 GACATTGAAC TTCCACATGA CCGAACTCAC AGTGGTGCCA 1041 GCTGACCTGG AGCTTCTCGC AAAGAAGTGC AAGTCACTAA 1081 TTTCATTGAA GATCAGTGAC TGTGACTTTT CAGATTTAAT 1121 TGGATTTTTC CGGATGGCTG CATCATTGCA AGAGTTTGCG 1161 GGAGGGGCAT TCATTGAGCA AGGGGAGCTC ACTAAGTATG 1201 GAAATGTTAA ATTCCCTTCA AGACTGTGCT CCTTAGGACT 1241 TACGTACATG GGGACAAACG AGATGCCCAT TATCTTCCCT 1281 TTCTCTGCAT TACTCAAGAA GCTGGACTTG CAGTACACTT 1321 TTCTCACCAC TGAAGATCAC TGCCAACTCA TTGCAAAATG 1361 TCCCAACTTA CTAGTTCTTG CGGTGAGGAA TGTGATTGGA 1401 GATAGAGGAT TAGGGGTTGT TGCAGACACA TGCAAGAAGC 1441 TACAAAGACT CAGAGTTGAG CGAGGAGATG ATGATCCAGG 1481 TTTGCAAGAA GAACAAGGAG GAGTCTCTCA AGTCGGGTTG 1521 ACAACTGTAG CCGTAGGATG CCGTGAACTG GAATACATAG 1561 CTGCCTATGT GTCTGATATC ACAAATGGGG CCCTGGAGTC 1601 TATTGGGACT TTCTGCAAAA ATCTTTGCGA CTTCCGTCTT 1641 GTCCTACTCG ATAGAGAAGA GAGGATAACA GATTTGCCCT 1681 TAGACAATGG TGTCCGTGCA CTGCTGAGGG GCTGCACGAA 1721 ACTTCGGAGG TTTGCTCTAT ACTTGAGACC AGGGGGACTT 1761 TCAGATACAG GCCTTGGCTA TATTGGACAG TACAGTGGAA 1801 TTATCCAATA CATGCTTCTG GGTAATGTTG GGGAAACAGA 1841 TGATGGTCTG ATCCGGTTTG CATTGGGGTG TGAGAACCTG 1881 CGGAAGCTTG AGCTAAGGAG TTGTTGCTTC AGTGAGCAAG 1921 CTTTAGCCCG CGCTATACGG AGTATGCCTT CCCTGAGATA 1961 CGTGTGGGTA CAGGGCTACA AGGCTTCTAA GACTGGTCAC 2001 GATCTCATGC TCATGGCCAG GCCCTTCTGG AACATAGAGT 2041 TTACACCTCC CAGTTCTGAG AATGCAAATC GAATGAGAGA 2081 AGATGGTGAA CCTTGTGTAG ATAGTCAAGC TCAGATACTT 2121 GCATACTACT CCCTTGCCGG GAAGAGGTCG GACTGCCCAC 2161 GATCTGTGGT TCCTTTGTAT CCTGCGTGAC TGTAAATACC 2201 GATATGGTAT CTCTCTGCTT CGTTCTTGCC TCTTGCCTTT 2241 TTTGGGTGAT ATGTTGATAT GTGGTTATTG TATGGGTCTA 2281 GAACTCTAGA TGGCTAGCTG CTATGTACCG TAATAAGCTA 2321 CTGGTAGCTG AGATGTACTG GAATAAGCAC TTCTATTTCC 2361 CACTCTACTA CTATCTAATC CTAGGAAGAT GTATACTAAG 2401 GAACACTCTG TGCCACTACT CCTTGCTTGT TCATGCTCCC 2441 GTCCTGGTTT GTTACCATTG GAGGTATAAG AATACCTGGT 2481 TTTGGCAGTC CTTAA

An example of a COI1 protein from Sorghum bicolor (sorghum) with NCBI accession number XP_002439888.1 (GI:242088111) has the following sequence (SEQ ID NO:47).

1 MGGEAPEPRR LTRALSIGGG DGGWVPEEML HLVMGFVEDP 41 RDREAASLVC RRWHRVDALS RKHVTVPFCY AVSPARLLAR 81 FPRLESLAIK GKPRAAMYGL IPDDWGAYAR PWVAELAAPL 121 ECLKALHLRR MVVTDDDLAE LVRARGHMLQ ELKLDKCTGF 161 STDGLRLVAR SCRSLRTLFL EECQINDKGS EWIHDLADGC 201 PVLTTLNFHM TELQVMPADL EFLARSCKSL ISLKISDCDV 241 SDLIGFFQFA TALEEFAGGT FNEQGELTMY GNVRFPSRLC 281 SLGLTFMGTN EMPIIFPFSA ILKKLDLQYT VLTTEDHCQL 321 IAKCPNLLVL AVRNVIGDRG LGVVADTCKK LQRLRIERGD 361 DEGGVQEEQG GVSQVGLTAI AVGCRELEYI AAYVSDITNG 401 ALESIGTFCK KLYDFRLVLL DREERITELP LDNGVRALLR 441 GCTKLRRFAL YLRPGGLSDA GLGYIGQCSG NIQYMLLGNV 481 GETDDGLFSF ALGCVNLRKL ELRSCCFSER ALALAILRMP 521 SLRYVWVQGY KASQTGRDLM LMARPFWNIE FTPPSSENAG 561 RLMEDGEPCV DSHAQILAYH SLAGKRLDCP QSVVPLYPA

A comparison of the Arabidopsis thaliana COI1 SEQ ID NO:1 sequence and the Sorghum bicolor COI1 SEQ ID NO:47 sequence is shown below, illustrating that the two proteins have at least 58% sequence identity. In addition, the location of the alanine at position 384 that can be replaced, for example with a valine, to generate a modified COI1 protein is also identified in bold and with underlining. As illustrated, the Sorghum bicolor COI1 SEQ ID NO:47 sequence has an alanine at the equivalent position (391). Such an alanine at position 391 of the Sorghum bicolor COI1 protein (SEQ ID NO:47) sequence can be modified and in some cases, it can be replaced with a valine.

58.4% identity in 570 residues overlap; Score: 1740.0; Gap frequency: 0.9% Seq1 18 DDVIEQVMTYITDPKDRDSASLVCRRWFKIDSETREHVTMALCYTATPDRLSRRFPNLRS Seq47 27 EEMLHLVMGFVEDPRDREAASLVCRRWHRVDALSRKHVTVPFCYAVSPARLLARFPRLES       **    ** **  ********   *   * ***   **   * **  *** * * Seq1 78 LKLKGKPRAAMFNLIPENWGGYVTPWVTEISNNLRQLKSVHFRRMIVSDLDLDRLAKARA Seq47 87 LAIKGKPRAAMYGLIPDDWGAYARPWVAELAAPLECLKALHLRRMVVTDDDLAELVRARG *  ********  ***  ** *  *** *    *  **  * *** * * **  *  ** Seq1 138 DDLETLKLDKCSGFTTDGLLSIVTHCRKIKTLLMEESSFSEKDGKWLHELAQHNTSLEVL Seq47 147 HMLQELKLDKCTGFSTDGLRLVARSCRSLRTLFLEECQINDKGSEWIHDLADGCPVLTTL   *  ****** ** ****      **   **  **     *   * * **     *  * Seq1 198 NFYMTEFAKISPKDLETIARNCRSLVSVKVGDFEILELVGFFKAAANLEEFCGGSLNEDI Seq47 207 NFHMTEL-QVMPADLEFLARSCKSLISLKISDCDVSDLIGFFQFATALEEFAGGTFNEQ- ** ***     * ***  ** * ** * *  *     * ***  *  **** **  ** Seq1 258 GMPEKYMNLVFPRKLCRLGLSYMGPNEMPILFPFAAQIRKLDLLYALLETEDHCTLIQKC Seq47 265 GELTMYGNVRFPSRLCSLGLTFMGTNEMPIIFPFSAILKKLDLQYTVLTTEDHCQLIAKC *    * *  **  ** ***  ** ***** *** *   **** *  * ***** ** ** Seq1 318 PNLEVLETRNVIGDRGLEVLAQYCKQLKRLRIERGADEQGMEDEEGLVSQRGLIALAQGC Seq47 325 PNLLVLAVRNVIGDRGLGVVADTCKKLQRLRIERGDDEGGVQEEQGGVSQVGLTAIAVGC *** **  ********* * *  ** * ******* ** *   * * *** ** * * ** Seq1 378 QELEYM A VYVSDITNESLESIGTYLKNLCDFRLVLLDREERITDLPLDNGVRSLLIGCKK Seq47 385 RELEYI A AYVSDITNGALESIGTFCKKLYDFRLVLLDREERITELPLDNGVRALLRGCTK  **** * *******  ******  * * ************** ******** ** ** * Seq1 438 LRRFAFYLRQGGLTDLGLSYIGQYSPNVRWMLLGYVGESDEGLMEFSRGCPNLQKLEMRG Seq47 445 LRRFALYLRPGGLSDAGLGYIGQCSGNIQYMLLGNVGETDDGLFSFALGCVNLRKLELRS ***** *** *** * ** **** * *   **** *** * **  *  ** ** *** * Seq1 498 CCFSERAIAAAVTKLPSLRYLWVQGYRASMTGQDLMQMARPYWNIELIP--SRRVPEVNQ Seq47 505 CCFSERALALAILRMPSLRYVWVQGYKASQTGRDLMLMARPFWNIEFTPPSSENAGRLME ******* * *    ***** ***** ** ** *** **** ****  *  * Seq1 556 QGEIREMEHPAHILAYYSLAGQRTDCPTTV Seq47 565 DGEPCVDSH-AQILAYHSLAGKRLDCPQSV  **     * * **** **** * ***  *

An example of a modified COI1 Sorghum bicolor protein with a valine instead of an alanine at position 391 has the following sequence (SEQ ID NO:48).

1 MGGEAPEPRR LTRALSIGGG DGGWVPEEML HLVMGFVEDP 41 RDREAASLVC RRWHRVDALS RKHVTVPFCY AVSPARLLAR 81 FPRLESLAIK GKPRAAMYGL IPDDWGAYAR PWVAELAAPL 121 ECLKALHLRR MVVTDDDLAE LVRARGHMLQ ELKLDKCTGF 161 STDGLRLVAR SCRSLRTLFL EECQINDKGS EWIHDLADGC 201 PVLTTLNFHM TELQVMPADL EFLARSCKSL ISLKISDCDV 241 SDLIGFFQFA TALEEFAGGT FNEQGELTMY GNVRFPSRLC 281 SLGLTFMGTN EMPIIFPFSA ILKKLDLQYT VLTTEDHCQL 321 IAKCPNLLVL AVRNVIGDRG LGVVADTCKK LQRLRIERGD 361 DEGGVQEEQG GVSQVGLTAI AVGCRELEYI  V AYVSDITNG 401 ALESIGTFCK KLYDFRLVLL DREERITELP LDNGVRALLR 441 GCTKLRRFAL YLRPGGLSDA GLGYIGQCSG NIQYMLLGNV 481 GETDDGLFSF ALGCVNLRKL ELRSCCFSER ALALAILRMP 521 SLRYVWVQGY KASQTGRDLM LMARPFWNIE FTPPSSENAG 561 RLMEDGEPCV DSHAQILAYH SLAGKRLDCP QSVVPLYPA

An example of a nucleotide (cDNA) sequence that encodes the Sorghum bicolor SEQ ID NO:47 COI1 protein (with NCBI cDNA accession number XM_002439843.1 (GI:242088110)) is shown below as SEQ ID NO:49.

1 CTCGTCCGTC CTCCTCTCCA CTCTCTCTTC TCCCTCCAAT 41 AATTCTCTCC TCTCTCTCTG CACTCTGCTT GCTCCACCTC 81 CAAGCACCAC CGAATCAGGG CCAGTGGGAG CAGCAGCAGC 121 AGCGAGTGGG AGCAGAGGAG GGCAGAGAAT CCCATGTCTC 161 CGCCCCTCGC TAGAGCAGAT CCTCGGCGAG CCGGGCGTGG 201 AGCTGCTTCG GTAGAAAAGC GAGCCAACTG AGCCTGCGAG 241 CGCCTGATCC GCCCGCGGCC CGATCGGGAT CGATGGGCGG 281 TGAGGCGCCG GAGCCCCGGC GGCTGACCCG CGCGCTGAGC 321 ATCGGCGGCG GCGACGGCGG CTGGGTCCCC GAGGAGATGC 361 TGCACCTGGT GATGGGGTTC GTCGAGGACC CGCGCGACCG 401 GGAGGCCGCG TCGCTGGTGT GCCGCCGGTG GCACCGCGTC 441 GACGCGCTGT CGCGGAAGCA CGTCACGGTG CCCTTCTGCT 481 ACGCCGTGTC CCCGGCGCGC CTGCTCGCGC GGTTCCCGCG 521 GCTCGAGTCG CTGGCCATCA AGGGGAAGCC CCGCGCGGCC 561 ATGTACGGCC TCATACCGGA CGACTGGGGC GCCTACGCCC 601 GCCCCTGGGT CGCCGAGCTC GCCGCGCCGC TCGAGTGCCT 641 CAAGGCGCTC CACCTCCGAC GCATGGTCGT CACGGACGAC 681 GACCTCGCCG AGCTCGTCCG TGCCAGGGGA CACATGCTGC 721 AGGAGCTCAA GCTCGACAAG TGCACCGGCT TCTCCACGGA 761 TGGACTCCGC CTCGTTGCGC GCTCCTGCAG ATCACTGAGA 801 ACTTTGTTTC TGGAAGAATG TCAAATTAAT GATAAAGGCA 841 GTGAATGGAT CCACGATCTT GCAGACGGTT GTCCTGTTCT 881 GACAACATTG AATTTCCACA TGACTGAGCT TCAAGTGATG 921 CCAGCTGACC TAGAGTTTCT TGCAAGGAGC TGCAAGTCAC 961 TGATTTCCTT GAAGATTAGC GACTGTGATG TTTCAGATTT 1001 GATAGGGTTC TTCCAATTTG CCACAGCACT GGAAGAATTT 1041 GCTGGAGGGA CATTCAATGA GCAAGGGGAA CTCACCATGT 1081 ATGGGAATGT CAGATTTCCA TCAAGACTAT GCTCCTTGGG 1121 ACTTACTTTC ATGGGAACAA ATGAAATGCC TATTATATTT 1161 CCTTTTTCTG CAATACTGAA GAAGCTGGAT TTGCAGTACA 1201 CTGTCCTCAC CACTGAAGAC CATTGCCAGC TTATTGCAAA 1241 ATGTCCGAAC TTACTAGTTC TCGCGGTGAG GAATGTGATT 1281 GGAGATAGAG GATTAGGAGT TGTTGCAGAT ACATGCAAGA 1321 AGCTCCAAAG GCTCAGAATT GAGCGAGGAG ACGATGAAGG 1361 AGGTGTGCAA GAAGAGCAGG GAGGGGTCTC TCAAGTGGGC 1401 TTGACGGCTA TAGCCGTCGG TTGCCGTGAA CTGGAATACA 1441 TAGCTGCCTA TGTGTCTGAT ATAACCAATG GGGCCCTGGA 1481 ATCTATCGGG ACATTCTGCA AAAAACTCTA TGACTTCCGG 1521 CTTGTTCTGC TTGATAGAGA AGAGAGGATA ACAGAATTGC 1561 CACTGGACAA TGGTGTCCGA GCTTTGTTGA GGGGCTGCAC 1601 CAAACTTCGG AGGTTTGCTC TGTACTTGAG ACCAGGAGGG 1641 CTCTCAGATG CAGGTCTCGG CTACATTGGA CAGTGCAGTG 1681 GAAACATCCA ATACATGCTT CTCGGTAATG TTGGGGAAAC 1721 TGATGATGGA TTGTTCAGTT TCGCATTGGG ATGCGTAAAC 1761 CTGCGGAAGC TTGAACTCAG GAGTTGTTGC TTCAGCGAGC 1801 GAGCTCTGGC CCTCGCCATA CTACGCATGC CTTCCCTGAG 1841 GTACGTATGG GTTCAGGGCT ACAAAGCGTC TCAAACCGGC 1881 CGAGACCTCA TGCTCATGGC GAGGCCCTTC TGGAACATAG 1921 AGTTTACACC TCCCAGTTCC GAGAACGCAG GTCGGTTGAT 1961 GGAAGATGGG GAACCTTGTG TAGATAGTCA TGCTCAGATA 2001 CTCGCATACC ACTCCCTCGC CGGTAAGAGG TTGGACTGCC 2041 CACAATCCGT GGTCCCTTTG TATCCTGCCT GAGTGTAAAT 2081 AGACTAAGCT GGTGTTTTTC TCCCTCATCC CTGCTTCCTT 2121 AGCCTCCTGG TCAACAAGAA CGATGTTGAT GACTTGATAT 2161 GTGGTTATTG TATGGATCTA GATGGCTAGC TGCTACGTAC 2201 TGTAATAAGC TACTAGTAGC TGAGATGTCC TGGAATAAGC 2241 CCTTGCTATT TTCGCCTGTA CTGCTATCTA ATCCTAGGAA 2281 GATGTATACT ACTAAGTAAC GGTGGAAGAT GTGAGTCTTG 2321 CTTGCTCGCC CTGATTTGTA CTATTGGAGG TATAAGAATA 2361 CCTGGGTTTT TGCCGCCTAC TTTGAGCATT GAGATGTGTC 2401 T

In some cases, the modified COI1 protein can have a sequence related to SEQ ID NO:1, 2, 5, 8, 10, 13, 16, 19, 22, 25, 28, 31, 33, 36, 39, 42, 45, or 48. However, the modified COI1 protein can have some sequence variation relative to SEQ ID NO:1, 2, 5, 8, 10, 13, 16, 19, 22, 25, 28, 31, 33, 36, 39, 42, 45, or 48. For example, a modified COI1 protein can have an amino acid sequence that has at least 90%, or at least 95%, or at least 96%, or at least 97%, at least 98%, or at least 99% sequence identity to SEQ ID NO:1, 2, 5, 8, 10, 13, 16, 19, 22, 25, 28, 31, 33, 36, 39, 42, 45, or 48.

Transformation of Plant Cells

Plant cells can be modified to include expression cassettes or transgenes that can express any of the modified COI1 proteins described herein. Such an expression cassette or transgene can include a promoter operably linked to a nucleic acid segment that encodes any of the modified COI1 proteins described herein.

Promoters provide for expression of mRNA from the COI1 nucleic acids. In some cases the promoter can be a COI1 native promoter. However, the promoter can in some cases be heterologous to the COI1 nucleic acid segment. In other words, such a heterologous promoter may not be naturally linked to such a COI1 nucleic acid segment. Instead, some expression cassettes and expression vectors have been recombinantly engineered to include a COI1 nucleic acid segment operably linked to a heterologous promoter. A COI1 nucleic acid is operably linked to the promoter, for example, when it is located downstream from the promoter.

A variety of promoters can be included in the expression cassettes and/or expression vectors. In some cases, the endogenous COIL promoter can be employed. Promoter regions are typically found in the flanking DNA upstream from the coding sequence in both prokaryotic and eukaryotic cells. A promoter sequence provides for regulation of transcription of the downstream gene sequence and typically includes from about 50 to about 2,000 nucleotide base pairs. Promoter sequences can also contain regulatory sequences such as enhancer sequences that can influence the level of gene expression. Some isolated promoter sequences can provide for gene expression of heterologous DNAs, that is a DNA different from the native or homologous DNA.

Promoters can be strong or weak, or inducible. A strong promoter provides for a high level of gene expression, whereas a weak promoter provides for a very low level of gene expression. An inducible promoter is a promoter that provides for the turning on and off of gene expression in response to an exogenously added agent, or to an environmental or developmental stimulus. For example, a bacterial promoter such as the P_(tac) promoter can be induced to vary levels of gene expression depending on the level of isothiopropylgalactoside added to the transformed cells. Promoters can also provide for tissue specific or developmental regulation. A strong promoter for heterologous DNAs can be advantageous because it provides for a sufficient level of gene expression for easy detection and selection of transformed cells and provides for a high level of gene expression when desired. In some cases, the promoter within such expression cassettes/vectors can be functional during plant development or growth.

Expression cassettes/vectors can include, but are not limited to, a plant promoter such as the CaMV 35S promoter (Odell et al., Nature. 313:810-812 (1985)), or others such as CaMV 19S (Lawton et al., Plant Molecular Biology. 9:315-324 (1987)), nos (Ebert et al., Proc. Natl. Acad. Sci. USA. 84:5745-5749 (1987)), Adh1 (Walker et al., Proc. Natl. Acad. Sci. USA. 84:6624-6628 (1987)), sucrose synthase (Yang et al., Proc. Natl. Acad. Sci. USA. 87:4144-4148 (1990)), α-tubulin, ubiquitin, actin (Wang et al., Mol. Cell. Biol. 12:3399 (1992)), cab (Sullivan et al., Mol. Gen. Genet. 215:431 (1989)), PEPCase (Hudspeth et al., Plant Molecular Biology. 12:579-589 (1989)) or those associated with the R gene complex (Chandler et al., The Plant Cell. 1:1175-1183 (1989)). Further suitable promoters include the poplar xylem-specific secondary cell wall specific cellulose synthase 8 promoter, cauliflower mosaic virus promoter, the Z10 promoter from a gene encoding a 10 kD zein protein, a Z27 promoter from a gene encoding a 27 kD zein protein, inducible promoters, such as the light inducible promoter derived from the pea rbcS gene (Coruzzi et al., EMBO J. 3:1671 (1971)) and the actin promoter from rice (McElroy et al., The Plant Cell. 2:163-171 (1990)). Seed specific promoters, such as the phaseolin promoter from beans, may also be used (Sengupta-Gopalan, Proc. Natl. Acad. Sci. USA. 83:3320-3324 (1985). Other promoters useful in the practice of the invention are available to those of skill in the art.

Alternatively, novel tissue specific promoter sequences may be employed in the practice of the present invention. cDNA clones from a particular tissue can be isolated and those clones which are expressed specifically in that tissue are identified, for example, using Northern blotting. Preferably, the gene isolated is not present in a high copy number, but is relatively abundant in specific tissues. The promoter and control elements of corresponding genomic clones can then be localized using techniques well known to those of skill in the art.

A COI1 nucleic acid can be combined with the promoter by standard methods to yield an expression cassette or transgene, for example, as described in Sambrook et al. (MOLECULAR CLONING: A LABORATORY MANUAL. Second Edition (Cold Spring Harbor, N.Y.: Cold Spring Harbor Press (1989); MOLECULAR CLONING: A LABORATORY MANUAL. Third Edition (Cold Spring Harbor, N.Y.: Cold Spring Harbor Press (2000)). Briefly, a plasmid containing a promoter such as the 35S CaMV promoter can be constructed as described in Jefferson (Plant Molecular Biology Reporter 5:387-405 (1987)) or obtained from Clontech Lab in Palo Alto, Calif. (e.g., pBI121 or pBI221). Typically, these plasmids are constructed to have multiple cloning sites having specificity for different restriction enzymes downstream from the promoter. The COI1 nucleic acids can be subcloned downstream from the promoter using restriction enzymes and positioned to ensure that the DNA is inserted in proper orientation with respect to the promoter so that the DNA can be expressed as sense or antisense RNA. Once the COI1 nucleic acid is operably linked to a promoter, the expression cassette so formed can be subcloned into a plasmid or other vector (e.g., an expression vector).

In some embodiments, a cDNA clone encoding a COI1 protein is synthesized, isolated, and/or obtained from a selected cell. In other embodiments, cDNA clones from other species (that encode a COI1 protein) are isolated from selected plant tissues. For example, the nucleic acid encoding a COI1 protein can be any nucleic acid with a coding region that hybridizes to SEQ ID NO:3 and that has COI1 activity. In another example, the COI1 nucleic acid can encode a COI1 protein with an amino acid sequence that has at least 90%, or at least 95%, or at least 96%, or at least 97%, at least 98%, or at least 99% sequence identity to SEQ ID NO:1, 2, 5, 8, 10, 13, 16, 19, 22, 25, 28, 31, 33, 36, 39, 42, 45, or 48. Using restriction endonucleases, the entire coding sequence for the COI1 nucleic acid is subcloned downstream of the promoter in a 5′ to 3′ sense orientation.

In some cases, an endogenous COI1 gene can be modified to generate plant cells and plants that can express a modified COI1 protein. Mutations can be introduced into COI1 plant genomes by introducing targeting vectors, T-DNA, transposons, nucleic acids encoding TALENS, CRISPR, or ZFN nucleases, and combinations thereof into a recipient plant cell to create a transformed cell.

In some cases the endogenous COI1 gene can be deleted and plant cells with such a deleted endogenous COI1 gene can be can be transformed to include a modified COI transgene, for example, by transformation of the plant cells with a COI1 expression cassette or expression vector.

The frequency of occurrence of cells taking up exogenous (foreign) DNA can sometimes be low. However, certain cells from virtually any dicot or monocot species can be stably transformed, and these cells can be regenerated into transgenic plants, through the application of the techniques disclosed herein. The plant cells, plants, and seeds can therefore be monocotyledons or dicotyledons.

The cell(s) that undergo transformation may be in a suspension cell culture or may be in an intact plant part, such as an immature embryo, or in a specialized plant tissue, such as callus, such as Type I or Type II callus.

Transformation of the cells of the plant tissue source can be conducted by any one of a number of methods available to those of skill in the art. Examples are: Transformation by direct DNA transfer into plant cells by electroporation (U.S. Pat. No. 5,384,253 and 5,472,869, Dekeyser et al., The Plant Cell. 2:591 602 (1990)); direct DNA transfer to plant cells by PEG precipitation (Hayashimoto et al., Plant Physiol. 93:857 863 (1990)); direct DNA transfer to plant cells by microprojectile bombardment (McCabe et al., Bio/Technology. 6:923 926 (1988), Gordon Kamm et al., The Plant Cell. 2:603 618 (1990); U.S. Pat. Nos. 5,489,520; 5,538,877; and 5,538,880) and DNA transfer to plant cells via infection with Agrobacterium. Methods such as microprojectile bombardment or electroporation can be carried out with “naked” DNA where the expression cassette may be simply carried on any E. coli derived plasmid cloning vector. In the case of viral vectors, it is desirable that the system retain replication functions, but lack functions for disease induction.

One method for dicot transformation, for example, involves infection of plant cells with Agrobacterium tumefaciens using the leaf disk protocol (Horsch et al., Science 227:1229 1231 (1985). Monocots such as Zea mays can be transformed via microprojectile bombardment of embryogenic callus tissue or immature embryos, or by electroporation following partial enzymatic degradation of the cell wall with a pectinase containing enzyme (U.S. Pat. Nos. 5,384,253; and 5,472,869). For example, embryogenic cell lines derived from immature Zea mays embryos can be transformed by accelerated particle treatment as described by Gordon Kamm et al. (The Plant Cell. 2:603 618 (1990)) or U.S. Pat. Nos. 5,489,520 ; 5,538,877 and 5,538,880, cited above. Excised immature embryos can also be used as the target for transformation prior to tissue culture induction, selection and regeneration as described in U.S. application Ser. No. 08/112,245 and PCT publication WO 95/06128. Furthermore, methods for transformation of monocotyledonous plants utilizing Agrobacterium tumefaciens have been described by Hiei et al. (European Patent 0 604 662, 1994) and Saito et al. (European Patent 0 672 752, 1995).

Methods such as microprojectile bombardment or electroporation are carried out with “naked” DNA where the expression cassette may be simply carried on any E. coli derived plasmid cloning vector. In the case of viral vectors, it is desirable that the system retain replication functions, but lack functions for disease induction.

The choice of plant tissue source for transformation will depend on the nature of the host plant and the transformation protocol. Useful tissue sources include callus, suspension culture cells, protoplasts, leaf segments, stem segments, tassels, pollen, embryos, hypocotyls, tuber segments, meristematic regions, and the like. The tissue source is selected and transformed so that it retains the ability to regenerate whole, fertile plants following transformation, i.e., contains totipotent cells. Type I or Type II embryonic maize callus and immature embryos are preferred Zea mays tissue sources. Selection of tissue sources for transformation of monocots is described in detail in U.S. application Ser. No. 08/112,245 and PCT publication WO 95/06128.

The transformation is carried out under conditions directed to the plant tissue of choice. The plant cells or tissue are exposed to the DNA or RNA carrying the targeting vector and/or other nucleic acids for an effective period of time. This may range from a less than one second pulse of electricity for electroporation to a 2-3 day co cultivation in the presence of plasmid bearing Agrobacterium cells. Buffers and media used will also vary with the plant tissue source and transformation protocol. Many transformation protocols employ a feeder layer of suspended culture cells (tobacco or Black Mexican Sweet corn, for example) on the surface of solid media plates, separated by a sterile filter paper disk from the plant cells or tissues being transformed.

Where one wishes to introduce DNA by means of electroporation, it is contemplated that the method of Krzyzek et al. (U.S. Pat. No. 5,384,253) may be advantageous. In this method, certain cell wall degrading enzymes, such as pectin degrading enzymes, are employed to render the target recipient cells more susceptible to transformation by electroporation than untreated cells. Alternatively, recipient cells can be made more susceptible to transformation, by mechanical wounding.

To effect transformation by electroporation, one may employ either friable tissues such as a suspension cell cultures, or embryogenic callus, or alternatively, one may transform immature embryos or other organized tissues directly. The cell walls of the preselected cells or organs can be partially degraded by exposing them to pectin degrading enzymes (pectinases or pectolyases) or mechanically wounding them in a controlled manner. Such cells would then be receptive to DNA uptake by electroporation, which may be carried out at this stage, and transformed cells then identified by a suitable selection or screening protocol dependent on the nature of the newly incorporated DNA.

A further advantageous method for delivering transforming DNA segments to plant cells is microprojectile bombardment. In this method, microparticles may be coated with DNA and delivered into cells by a propelling force. Exemplary particles include those comprised of tungsten, gold, platinum, and the like.

It is contemplated that in some instances DNA precipitation onto metal particles would not be necessary for DNA delivery to a recipient cell using microprojectile bombardment. In an illustrative embodiment, non-embryogenic cells were bombarded with intact cells of the bacteria E. coli or Agrobacterium tumefaciens containing plasmids with either the β-glucoronidase or bar gene engineered for expression in maize. Bacteria were inactivated by ethanol dehydration prior to bombardment. A low level of transient expression of the β-glucoronidase gene was observed 24-48 hours following DNA delivery. In addition, stable transformants containing the bar gene were recovered following bombardment with either E. coli or Agrobacterium tumefaciens cells. It is contemplated that particles may contain DNA rather than be coated with DNA. Hence it is proposed that particles may increase the level of DNA delivery but are not, in and of themselves, necessary to introduce DNA into plant cells.

An advantage of microprojectile bombardment, in addition to being an effective means of reproducibly stably transforming monocots, is that the isolation of protoplasts (Christou et al., PNAS. 84:3962 3966 (1987)), the formation of partially degraded cells, or the susceptibility to Agrobacterium infection is not required. An illustrative embodiment of a method for delivering DNA into maize cells by acceleration is a Biolistics Particle Delivery System, which can be used to propel particles coated with DNA or cells through a screen, such as a stainless steel or Nytex screen, onto a filter surface covered with maize cells cultured in suspension (Gordon Kamm et al., The Plant Cell. 2:603 618 (1990)). The screen disperses the particles so that they are not delivered to the recipient cells in large aggregates. It is believed that a screen intervening between the projectile apparatus and the cells to be bombarded reduces the size of projectile aggregate and may contribute to a higher frequency of transformation, by reducing damage inflicted on the recipient cells by an aggregated projectile.

For bombardment, cells in suspension are preferably concentrated on filters or solid culture medium. Alternatively, immature embryos or other target cells may be arranged on solid culture medium. The cells to be bombarded are positioned at an appropriate distance below the macroprojectile stopping plate. If desired, one or more screens are also positioned between the acceleration device and the cells to be bombarded. Through the use of techniques set forth here in one may obtain up to 1000 or more foci of cells transiently expressing a marker gene. The number of cells in a focus which express the exogenous gene product 48 hours post bombardment often range from about 1 to 10 and average about 1 to 3.

In bombardment transformation, one may optimize the prebombardment culturing conditions and the bombardment parameters to yield the maximum numbers of stable transformants. Both the physical and biological parameters for bombardment can influence transformation frequency. Physical factors are those that involve manipulating the DNA/microprojectile precipitate or those that affect the path and velocity of either the macroprojectiles or microprojectiles. Biological factors include all steps involved in manipulation of cells before and immediately after bombardment, the osmotic adjustment of target cells to help alleviate the trauma associated with bombardment, and also the nature of the transforming DNA, such as linearized DNA or intact supercoiled plasmid DNA.

One may wish to adjust various bombardment parameters in small scale studies to fully optimize the conditions and/or to adjust physical parameters such as gap distance, flight distance, tissue distance, and helium pressure. One may also minimize the trauma reduction factors (TRFs) by modifying conditions which influence the physiological state of the recipient cells and which may therefore influence transformation and integration efficiencies. For example, the osmotic state, tissue hydration and the subculture stage or cell cycle of the recipient cells may be adjusted for optimum transformation. Execution of such routine adjustments will be known to those of skill in the art.

Examples of plants and/or plant cells that can be modified as described herein include alfalfa (e.g., forage legume alfalfa), algae, apple, avocado, balsam, barley, broccoli, Brussels sprouts, cabbage, canola, cassava, cauliflower, cocoa, cole vegetables, collards, corn, cottonwood, crucifers, earthmoss, grain legumes, grasses (e.g., forage grasses), jatropa, kale, kohlrabi, maize, miscanthus, moss, mustards, nut, nut sedge, oats, oil firewood trees, oilseeds, peach, peanut, poplar, potato, radish, rape, rapeseed, rice, rutabaga, sorghum, soybean, sugar beets, sugarcane, sunflower, switchgrass, tobacco, tomato, turnips, and wheat. In some embodiments, the plant is a Brassicaceae or other Solanaceae species. In some embodiments, the plant or cell can be a maize plant or maize cell. In some cases, the plant or plant cell can be a soybean plant or plant cell. In some embodiments, the plant is not a species of Arabidopsis, for example, in some embodiments, the plant is not Arabidopsis thaliana.

An exemplary embodiment of methods for identifying transformed cells involves exposing the bombarded cultures to a selective agent, such as a metabolic inhibitor, an antibiotic, herbicide or the like. Cells which have been transformed and have stably integrated a marker gene conferring resistance to the selective agent used, will grow and divide in culture. Sensitive cells will not be amenable to further culturing.

To use the bar-bialaphos or the EPSPS-glyphosate selective system, bombarded tissue is cultured for about 0-28 days on nonselective medium and subsequently transferred to medium containing from about 1-3 mg/l bialaphos or about 1-3 mM glyphosate, as appropriate. While ranges of about 1-3 mg/l bialaphos or about 1-3 mM glyphosate can be employed, it is proposed that ranges of at least about 0.1-50 mg/I bialaphos or at least about 0.1-50 mM glyphosate will find utility in the practice of the invention. Tissue can be placed on any porous, inert, solid or semi-solid support for bombardment, including but not limited to filters and solid culture medium. Bialaphos and glyphosate are provided as examples of agents suitable for selection of transformants, but the technique of this invention is not limited to them.

An example of a screenable marker trait is the red pigment produced under the control of the R-locus in maize. This pigment may be detected by culturing cells on a solid support containing nutrient media capable of supporting growth at this stage and selecting cells from colonies (visible aggregates of cells) that are pigmented. These cells may be cultured further, either in suspension or on solid media. The R-locus is useful for selection of transformants from bombarded immature embryos. In a similar fashion, the introduction of the C1 and B genes will result in pigmented cells and/or tissues.

The enzyme luciferase is also useful as a screenable marker in the context of the present invention. In the presence of the substrate luciferin, cells expressing luciferase emit light which can be detected on photographic or X-ray film, in a luminometer (or liquid scintillation counter), by devices that enhance night vision, or by a highly light sensitive video camera, such as a photon counting camera. All of these assays are nondestructive and transformed cells may be cultured further following identification. The photon counting camera is especially valuable as it allows one to identify specific cells or groups of cells which are expressing luciferase and manipulate those in real time.

It is further contemplated that combinations of screenable and selectable markers may be useful for identification of transformed cells. For example, selection with a growth inhibiting compound, such as bialaphos or glyphosate at concentrations below those that cause 100% inhibition followed by screening of growing tissue for expression of a screenable marker gene such as luciferase would allow one to recover transformants from cell or tissue types that are not amenable to selection alone. In an illustrative embodiment embryogenic Type II callus of Zea mays L. can be selected with sub-lethal levels of bialaphos. Slowly growing tissue was subsequently screened for expression of the luciferase gene and transformants can be identified.

Regeneration and Seed Production

Cells that survive the exposure to the selective agent, or cells that have been scored positive in a screening assay, are cultured in media that supports regeneration of plants. One example of a growth regulator that can be used for such purposes is dicamba or 2,4-D. However, other growth regulators may be employed, including NAA, NAA+ 2,4-D or perhaps even picloram. Media improvement in these and like ways can facilitate the growth of cells at specific developmental stages. Tissue can be maintained on a basic media with growth regulators until sufficient tissue is available to begin plant regeneration efforts, or following repeated rounds of manual selection, until the morphology of the tissue is suitable for regeneration, at least two weeks, then transferred to media conducive to maturation of embryoids. Cultures are typically transferred every two weeks on this medium. Shoot development signals the time to transfer to medium lacking growth regulators.

The transformed cells, identified by selection or screening and cultured in an appropriate medium that supports regeneration, can then be allowed to mature into plants. Developing plantlets are transferred to soilless plant growth mix, and hardened, e.g., in an environmentally controlled chamber at about 85% relative humidity, about 600 ppm CO₂, and at about 25-250 microeinsteins/sec·m² of light. Plants can be matured either in a growth chamber or greenhouse. Plants are regenerated from about 6 weeks to 10 months after a transformant is identified, depending on the initial tissue. During regeneration, cells are grown on solid media in tissue culture vessels. Illustrative embodiments of such vessels are petri dishes and Plant Con™. Regenerating plants can be grown at about 19° C. to 28° C. After the regenerating plants have reached the stage of shoot and root development, they may be transferred to a greenhouse for further growth and testing.

Mature plants are then obtained from cell lines that are known to have the mutations. In some embodiments, the regenerated plants are self-pollinated. In addition, pollen obtained from the regenerated plants can be crossed to seed grown plants of agronomically important inbred lines. In some cases, pollen from plants of these inbred lines is used to pollinate regenerated plants. The trait is genetically characterized by evaluating the segregation of the trait in first and later generation progeny. The heritability and expression in plants of traits selected in tissue culture are of particular importance if the traits are to be commercially useful.

Regenerated plants can be repeatedly crossed to inbred plants in order to introgress the mutations into the genome of the inbred plants. This process is referred to as backcross conversion. When a sufficient number of crosses to the recurrent inbred parent have been completed in order to produce a product of the backcross conversion process that is substantially isogenic with the recurrent inbred parent except for the presence of the introduced expression cassette encoding a modified COI1, the plant is self-pollinated at least once in order to produce a homozygous backcross converted inbred containing the mutations. Progeny of these plants are true breeding.

Alternatively, seed from transformed mutant plant lines regenerated from transformed tissue cultures is grown in the field and self-pollinated to generate true breeding plants.

Seed from the fertile transgenic plants can then be evaluated for the presence of the desired COI1 genomic modification (e.g., mutation), e.g., the desired COI1 expression cassette, and/or the expression of the desired modified COI1 protein. Transgenic plant and/or seed tissue can be analyzed using standard methods such as SDS polyacrylamide gel electrophoresis, liquid chromatography (e.g., HPLC) or other means of detecting a mutation.

Once a transgenic plant with a mutant sequence and having improved growth and pathogen resistance is identified, seeds from such plants can be used to develop true breeding plants. The true breeding plants are used to develop a line of plants with improved growth and pathogen resistance relative to wild type, and acceptable insect resistance while still maintaining other desirable functional agronomic traits. Adding the mutation to other plants can be accomplished by back-crossing with this trait and with plants that do not exhibit this trait and studying the pattern of inheritance in segregating generations. Those plants expressing the target trait (e.g., herbicide and pathogen resistance, good growth) in a dominant fashion are preferably selected. Back-crossing is carried out by crossing the original fertile transgenic plants with a plant from an inbred line exhibiting desirable functional agronomic characteristics while not necessarily expressing the trait of increased herbicide and pathogen resistance and good plant growth. The resulting progeny are then crossed back to the parent that expresses the increased herbicide and pathogen resistance and good plant growth. The progeny from this cross will also segregate so that some of the progeny carry the trait and some do not. This back-crossing is repeated until an inbred line with the desirable functional agronomic traits, and with expression of the trait involving an increase in herbicide and pathogen resistance and good plant growth. Such herbicide and pathogen resistance as well as good plant growth can be expressed in a dominant fashion.

The new transgenic plants can also be evaluated for a battery of functional agronomic characteristics such as growth, lodging, kernel hardness, yield, resistance to disease and insect pests, drought resistance, and/or herbicide resistance.

Plants that may be improved by these methods include but are not limited to agricultural plants of all types, oil and/or starch plants (canola, potatoes, lupins, sunflower and cottonseed), forage plants (alfalfa, clover and fescue), grains (maize, wheat, barley, oats, rice, sorghum, millet and rye), grasses (switchgrass, prairie grass, wheat grass, sudangrass, sorghum, straw-producing plants), softwood, hardwood and other woody plants (e.g., those used for paper production such as poplar species, pine species, and eucalyptus). In some embodiments the plant is a gymnosperm. Examples of plants useful for pulp and paper production include most pine species such as loblolly pine, Jack pine, Southern pine, Radiata pine, spruce, Douglas fir and others. Hardwoods that can be modified as described herein include aspen, poplar, eucalyptus, and others. Plants useful for making biofuels and ethanol include corn, grasses (e.g., miscanthus, switchgrass, and the like), as well as trees such as poplar, aspen, willow, and the like. Plants useful for generating dairy forage include legumes such as alfalfa, as well as forage grasses such as bromegrass, and bluestem.

Determination of Stably Transformed Plant Tissues

To confirm the presence of COI1 mutations and/or a COI1 expression cassette in the regenerating plants, or seeds or progeny derived from the regenerated plant, a variety of assays may be performed. Such assays include, for example, molecular biological assays available to those of skill in the art, such as Southern and Northern blotting and PCR; biochemical assays, such as detecting the presence of a protein product, e.g., by immunological means (ELISAs and Western blots) or by enzymatic function; plant part assays, such as leaf, seed or root assays; and also, by analyzing the phenotype of the whole regenerated plant.

Whereas DNA analysis techniques may be conducted using DNA isolated from any part of a plant, RNA may only be expressed in particular cells or tissue types and so RNA for analysis can be obtained from those tissues. PCR techniques may also be used for detection and quantification of RNA produced from introduced COI1 mutation(s) or of RNA expressed from an introduced expression cassette encoding a modified COI1. For example, PCR also be used to reverse transcribe RNA into DNA, using enzymes such as reverse transcriptase, and then this DNA can be amplified through the use of conventional PCR techniques.

For example, if no amplification of COI1 mRNAs is observed, then a deletion mutation has successfully been introduced.

Information about mutations can also be obtained by primer extension or single nucleotide polymorphism (SNP) analysis.

Further information about the nature of the RNA product may be obtained by Northern blotting. This technique will demonstrate the presence of an RNA species and give information about the integrity of that RNA. The presence of some mutations can be detected by Northern blotting. The presence or absence of an RNA species (e.g., COI1 RNA) can also be determined using dot or slot blot Northern hybridizations. These techniques are modifications of Northern blotting and also demonstrate the presence or absence of an RNA species.

While Southern blotting and PCR may be used to detect the presence of mutations or the presence of a COI1 expression cassette, they do not provide information as to whether the preselected DNA segment is being expressed. Expression may be evaluated by specifically identifying the protein products of the introduced COI1 expression cassette or the introduced mutations, by detecting expression of modified COI proteins, or evaluating the phenotypic changes brought about by such mutation.

Assays for the production and identification of specific proteins may make use of physical-chemical, structural, functional, or other properties of the proteins. Unique physical-chemical or structural properties allow the proteins to be separated and identified by electrophoretic procedures, such as native or denaturing gel electrophoresis or isoelectric focusing, or by chromatographic techniques such as ion exchange, liquid chromatography or gel exclusion chromatography. The unique structures of individual proteins offer opportunities for use of specific antibodies to detect their presence in formats such as an ELISA assay. Combinations of approaches may be employed with even greater specificity such as Western blotting in which antibodies are used to locate individual gene products, or the absence thereof, that have been separated by electrophoretic techniques. Additional techniques may be employed to absolutely confirm the identity of a mutation such as evaluation by screening for reduced transcription (or no transcription) of wild type COI1 and/or modified (mutant) COI1 mRNAs, by screening for wild type and/or mutant (modified) COI1 mRNA or COI1 protein expression. Amino acid sequencing following purification can also be employed. The Examples of this application also provide assay procedures for detecting and quantifying infection and plant growth. Other procedures may be additionally used.

The expression of a gene product can also be determined by evaluating the phenotypic results of its expression. These assays also may take many forms including but not limited to analyzing changes in the resistance to infection, resistance to herbicides, growth characteristics, or other physiological properties of the plant. Expression of selected DNA segments encoding different amino acids or having different sequences and may be detected by amino acid analysis or sequencing.

The following Examples describe some of the experiments performed in the development of the invention.

EXAMPLE 1 Materials and Methods

This Example illustrates some of the materials and methods employed during development of the invention.

All experiments were performed three or more times with similar results. For computer modeling, coordinates for JA-Ile or coronatine (COR) were obtained from the crystal structures of COI1-JA-Ile/COR-JAZ degron peptide complex (PDB ID codes 3OGL and 3OGK, respectively). Structures of (3R,7S) JA-Ile and coronatine are shown below:

In Y2H and in planta assays, the relative potencies of different ligands used (COR, MeJA, and JA-Ile) were standardized before a new set of experiments. Because of the limited amounts of JA-Ile available for this study, other forms of JA were used if the use of JA-Ile was not absolutely needed. For example, MeJA can be converted to JA-Ile in planta and is commonly used in the study of JA signaling (Staswick et al., Plant Cell 16(8): 2117-2127 (2004)). Therefore, MeJA was used instead of JA-Ile, for in planta assays.

Computational Modeling

Coordinates for JA-Ile or COR were obtained from the crystal structures of COI1-JA-Ile/COR-JAZ degron peptide complex (PDB ID codes 3OGL and 3OGK, respectively) and the hydrogen atoms were added using xleap module in the Ambertools. Force field parameters and charges were derived using Antechamber module and GAFF in Ambertools (Wand et al., Antechamber, An Accessory Software Package for Molecular Mechanical Calculation. Abstracts of Papers, 222nd National Meeting of the American Chemical Society, Chicago, Ill., Aug. 2630, 2001; American Chemical Society: Washington, DC:U403 (2001)).

The force field ff99SB was used to represent the molecular mechanical potential. The system consisting of COR or JA-Ile along with COI1 and part of the JAZ degron peptide were minimized in two stages using a combination of steepest descent (15,000 steps) and conjugated gradient (5,000 steps) methods (Case et al., AMBER 12 (University of California, San Francisco). Available at ambermd.org/doc 12/Amber12.pdf. (2012)). A strong positional restraint (20 kcal/mole) was applied on all protein and ligand heavy atoms during the first stage of minimization. The protein-ligand complex was minimized again in the second stage, without any positional restraint. In silico mutations for A86 and A384 were introduced in COI1 using Pymol (DeLano Scientific).

Gene Cloning, Site-Direct Mutagenesis, and Plasmid Construction

The coding sequences of AtCOI1 and AtJAZ9 were amplified from total mRNA extract of Arabidopsis Col-0 leaf tissue and cloned into the pCR2.1-TOPO plasmid or pENTR-D TOPO Gateway entry vector (Life Technologies). Specific mutations were introduced into the AtCOI1 coding sequence directly through the QuickChangeII site directed mutagenesis kit (Agilent Technologies). For Y2H assays, the bait and prey vectors pGILDA and pB42AD (Clontech) were first converted to Gateway cloning-compatible pGILDAattR and pB42ADattR vectors by inserting an attR cassette (Life Technologies) into their multiple cloning sites, respectively. Next, the wild-type and mutated COI1 coding sequences in the entry vector were recombined into pGILDAattR using LR ClonaseII (Life Technologies) to generate C-terminal fusions to the LexA DNA binding domain. The JAZ9 coding sequences were recombined into pB42ADattR to generate C-terminal fusions to the B42 transcriptional activation domain.

For plant transformation, the AtCOI1 without stop codon was first cloned into pENTR4A to create pENCOI1C. Next, the native promoter of AtCOI1 (pCOI1; a genomic DNA fragment 1,807 bp upstream of the COI1 start codon) was cloned into pENCOI1C to create a pENpCOI1:COI1 entry vector. COI1A384V was introduced into this vector to create pENpCOI1:COI1A384V. Both pCOI1: COI1WT and pCOI1:COI1A384V were recombined into pGWB516 vector (containing a hygromycin resistance gene and a C-terminal 4×c-Myc epitope tag) (Nakagawa et al., Biol Rev Camb Philos Soc 82(4):591-605 (2007)) using LR ClonaseII. Confirmed constructs were introduced into Agrobacterium tumefaciens (GV3101) by electroporation.

Y2H Assays for Protein-Protein Interaction

For some Y2H experiments JA-Ile was used, because JA or MeJA are not active in yeast (Thines et al., Nature 448(7154):661-665 (2007); Melotto et al., Plant J 55(6):979-988 (2008)).

Yeast EGY48 strain carrying the p8Op:LacZ reporter plasmid was co-transformed with pGilda:COI1 (or COI1 mutants) and pB42AD:JAZ9 (or other JAZs) (Clontech). Colonies were selected on SD minimal plates (BD Biosciences) supplemented with the—uracil (U)/-tryptophan (W)/-histidine (H) amino acid drop out solution (Clontech). Yeast colonies were cultured overnight in liquid SD-UWH medium, harvested, washed twice in sterile water, and the absorbance (OD₆₀₀) of the cultures was adjusted to 0.2 in liquid SD galactose/raffinose-UWH medium (BD Biosciences).

For Y2H assays on plates, 10-μL culture was spotted onto SD galactose/raffinose-UWH plates with 80 μg/mL X-gal and 10 μM COR (Sigma-Aldrich). Blue color indicated protein-protein interactions after 5-7 days of incubation at 30° C.

For liquid Y2H assays, cultures were supplemented with designated concentrations of JA-Ile (10 or 30 μM), COR (1 μM), or DMSO. After 16-h incubation with ligands, the liquid cultures were processed through the Beta-Glo Assay system (Promega) for detecting the β-galactosidase activity. The JA-Ile stock consisted of cis- and trans-isomers, the cis-form being more active. Initial chemical analysis showed 6.8% of the cis-form after synthesis. Protein expression in yeast was detected using anti-LexA antibody (1:5,000; Upstate Biotechnology) for detection of COI1 expression from pGilda vector and anti-HA (1:5,000; Roche Life Science) antibody for detection of JAZ9 expression in pB42AD vector.

Arabidopsis Transformation and Screening

pCOI1:COI1WT/A384V-4xc-Myc constructs were transformed into coil-30 mutant Arabidopsis plants (Yang et al., Proc Natl Acad Sci USA 109(19): E1192-E1200. (2012)). Because homozygous coi1-30 plants are male-sterile, heterozygous plants were identified through genotyping and used for A. turnefaciens-mediated Arabidopsis transformation, Half-strength Murashige and Skoog (MS) medium with 50 μg/mL hygromycin was used to select transgenic T1 seedlings containing the pCOI1:COI1WT/A384V-4xc-Myc transgene. Hygromycin-resistant seedlings were transplanted and genotyping was carried out to identify transgenic plants with the homozygous coil-30 background. Further screening of T2 or T3 plants were performed for homozygous transgene. Primers used were:

SALK035548_LP1: (SEQ ID NO: 50) CGAATAAATCACACAGCTTATTGG, SALK035548_RP1: (SEQ ID NO: 51) GATATGGTTCTTTGTACAACGACG, LBb1.3: (SEQ ID NO: 52) ATTTTGCCGATTTCGGAAC, and SALK035548_RP: (SEQ ID NO: 53) CTGCAGTGTGTAACGATGCTC. Protein Immunoblot Analysis

Proteins were extracted from 10-day-old to 12-day-old seedlings by protein extraction buffer (50 mM Tris.HCl, pH7.5, 150mMNaCl, 1% Nonidet P-40, 1% sodium deoxycholate, 0.1% SDS). Protein concentrations were measured using the RC/DC protein assay kit (Bio-Rad) with BSA as the standard (Bio-Rad). Protein samples with the same total protein concentration were used for immunoblot with rabbit polyclonal anti-c-Myc primary antibodies (1:5,000, Clontech) and goat anti-rabbit secondary antibody (1:20,000).

Coreceptor Pull-Down Assay

Pull-down assays were performed with protein extracts from 4-mg pCOI1:COI1WT/A384V-4×c-Myc plants and 25 μg recombinant MBP-JAZ9-8×His. Assays were performed in the presence of JA-Ile or COR at various concentrations and incubated for 30 min at 4° C. in the binding buffer (Katsir et al., Proc Natl Acad Sci USA 105(19):7100-7105 (2008)). Eighty microliters of Ni resin (Invitrogen) were added, followed by an additional 15-min incubation period at 4° C. MBP-JAZ9-8×Hisbound Ni resin was washed three times on microcentrifuge spin columns with 0.25 mL binding buffer at 4° C. MBP-JAZ9-8×His was eluted from the resin with 100 μL of 300 mM imidazole. Proteins bound to MBP-JAZ9-8×His were analyzed by immunoblotting for the presence of COI1WT/A384V-4×c-Myc using anti-cMyc antibody. MBP-JAZ9-8×His recovered by the Ni affinity resin was detected by Coomassie blue staining.

RNA Isolation and qPCR Assays

Col-0 and transgenic seeds were germinated on half-strength MS medium. Five-day-old seedlings were transferred into liquid half-strength MS medium. Segregating coil-30 seeds were germinated on half-strength MS medium with 10 μM MeJA. and MeJA-resistant 5-d-old seedlings were transferred into liquid half-strength MS medium. Next, 10 μM MeJA (Sigma), 0.2 μM COR or 0.1% DMSO were applied to 12-d-old seedlings. Samples were collected after 3 h and total RNA was extracted using Qiagen RNeasy Mini kit (Qiagen). M-MLV Reverse transcriptase (Life Technologies) and SYBR Green master mix (Life Technologies) were used for reverse-transcription and real-time PCR. Primers used were:

PP2AA3_qRT_F1: (SEQ ID NO: 54) GGTTACAAGACAAGGTTCACTC, PP2AA3_qRT_R1: (SEQ ID NO: 55) CATTCAGGACCAAACTCTTCAG, JAZ9_qRT_F1: (SEQ ID NO: 56) ATGAGGTTAACGATGATGCTG, JAZ9_qRT_R1: (SEQ ID NO: 57) CTTAGCCTCCTGGAAATCTG, PR1_qRT_F1: (SEQ ID NO: 58) GGCTAACTACAACTACGCTG, PR1_qRT_R1: (SEQ ID NO: 59) TCTCGTTCACATAATTCCCAC, SID2_qRT_F2: (SEQ ID NO: 60) ACTTACTAACCAGTCCGAAAGACGA, and SID2_qRT_R2: (SEQ ID NO: 61) ACAACAACTCTGTCACATATACCGT. Root Growth Inhibition Assays

Col-0, segregating COI1-30, transgenic COI1WT, and COI1A384V seeds were surface-sterilized, cold-stratified, and germinated on half-strength MS agar media containing MeJA, COR, or DMSO at the indicated concentrations. Seedlings were grown under long-day light conditions (16-h light at 100 μE·m²·s, and 8-h dark) for 10-12 days before scanning images of roots. Root lengths were measured using ImageJ software (see website at rsbweb.nih.gov/ij/).

Bacterial Infection Assays

The Pseudomonas syringae infection assays in Arabidopsis were performed as described by Yao et al. (Methods Mol Biol 1011:63-81 (2013)). In brief, 4- to 5-wk-old (12-h light/12-h dark) Arabidopsis plants were dip-inoculated with bacterial suspension (1×10⁸ cfu/mL Pst DC3000 or Psm ES4326 in 0.25 mM MgCl₂ solution with 0.025% Silwet-77) or syringe-infiltrated with bacterial suspension (1×10⁶ cfu/mL Pst DC3118 or DB29 in 0.25 mM MgCl₂ solution). Bacterial growth was determined by serial dilutions of plant extracts 3 or 4 days after inoculation. Homozygous COI1-30 plants were selected by genotyping before bacterial infection.

Insect Feeding Assays

Insect bioassays were performed as described by Herde et al. (Methods Mol Biol 1011:51-61 (2013)). Briefly, eggs of Spodoptera exigua were obtained from Benzon Research, and four neonate Spodoptera exigua larvae were transferred to the center of each 6-wk-old Arabidopsis host plant. Plants were grown under 8-hour light (100 μE·m²·s) and 16-h dark and covered with cup cages. Larval weights were determined after 9-12 days of feeding.

EXAMPLE 2 Targeted COI1 Alanine Substitution Mutagenesis

Higher plants synthesize different forms of JA, including the most bioactive form jasmonoyl-L-isoleucine (JA-Ile). Targeted alanine substitution mutagenesis of the COI1 protein was conducted to identify amino acid residues that can differentially affect the actions of JA-Ile against COR. At the onset of this study, the crystal structure of the COI1-JAZ coreceptor was not available. However, the crystal structure of the TIR1-AUX/IAA [for TRANSPORT INHIBITOR RESPONSE 1 (TIR1)-AUXIN/INDOLE 3-ACETIC ACID (AUX/IAA)] coreceptor involved in the perception of the plant hormone auxin was available (Tan et al., Nature 446(7136):640-645 (2007)). Auxin and JA signaling pathways are highly analogous in hormone sensing and response (Pauwels et al., Nature 464(7289):788-791 (2010); Santner & Estelle, Nature 459(7250):1071-1078 (2009)). Comparative genomic analysis suggested that auxin and JA signaling pathways may have originated from a common ancestor that duplicated and diverged into TIR1 and COI1 for different hormone signaling pathways (Wang et al., Plant Physiol 167(3):872-886 (2015)).

The inventors hypothesized that ligand-binding surfaces in COI1 may be similarly positioned to those in TIR1, and key differences in these conserved residues might confer specificity to the differential recognition of the respective ligands (i.e., JA-Ile/COR vs. auxin). Based on these initial criteria, thirty-two amino acids were selected for site-direct mutagenesis to alanine (Table 1).

TABLE 1 Amino acids for Site-Directed Mutagenesis to Alanine Role in COI1 Homologous Role in TIR1 COI1 Interaction ligand binding TIR1 amino ligand binding amino acid with JAZ9* pocket^(†) acid^(‡) pocket^(‡) Histidine 54^(§) +++ PO₄ contacting Lysine Not known Serine 77^(§) +++ PO₄ contacting Serine Not known Lysine 79^(§) +++ PO₄ contacting Glutamate Not known Lysine 81 +++ PO₄ contacting Lysine IP6 coordination Arginine 85 +++ JA-Ile and PO₄ Histidine Auxin binding, IP6 contacting coordination Methionine 88 No JAZ1 and PO₄ Aspartate Aux/IAA binding contacting Phenylalanine 89 No JA-Ile and JAZ1 Phenylalanine Auxin and contacting AUX/IAA binding Leucine 91 No JA-Ile and JAZ1 Leucine Aux/IAA binding contacting Histidine 118^(§) +++ PO₄ contacting Arginine Not known Arginine 121 No PO₄ contacting Arginine IP6 coordination Lysine 144^(§) +++ PO₄ contacting Valine Not known Lysine 147 ++++ PO₄ contacting Serine Aux/IAA binding Glutamate 173 ++ JAZ1 contacting Glutamate Aux/IAA binding Methionine 201^(§) +++ JAZ1 contacting Cysteine Not known Leucine 301^(§) +++ JAZ1 contacting Serine Not known Tyrosine 302^(§) No JAZ1 contacting Tyrosine Not known Arginine 326^(§) No JAZ1 contacting Leucine Not known Arginine 348 No JA-Ile, JAZ1 and Arginine IP6 coordination PO₄ contacting Arginine 351 No JAZ1 contacting Proline AUX/IAA binding Aspartate 354 No JAZ1 contacting Glutamate AUX/IAA binding Glutamate 355 +++ JAZ1 contacting Proline AUX/IAA binding Glutamine 356 +++ Non Phenylalanine AUX/IAA binding Glycine 357 ++ Non Valine AUX/IAA binding Tyrosine 386 No JA-Ile and JAZ1 Phenylalanine Auxin and contacting AUX/IAA binding Aspartate 407 No Non Arginine IP6 coordination Arginine 409 No JA-Ile and PO₄ Arginine Auxin and contacting AUX/IAA binding Leucine 410 No Non Leucine Auxin binding Valine 411 No JA-Ile and JAZ1 Cysteine Auxin and contacting AUX/IAA binding Leucine 412 No Non Isoleucine AUX/IAA binding Leucine 413 No JAZ1 contacting Isoleucine AUX/IAA binding Arginine 415 ++ Non Proline AUX/IAA binding Arginine 440 ++ Non Arginine IP6 coordination Phenylalanine 443 No Non Leucine Auxin binding Tyrosine 444^(§) No JA-Ile and JAZ1 None Not known contacting Tryptophan 467 +++ Non Methionine IP6 coordination Leucine 469 No JA-Ile contacting Serine Auxin binding Leucine 470 No Non Valine Auxin binding Tyrosine 472 +++ PO₄ contacting Phenylalanine AUX/IAA binding Glutamine 491 +++ Non Arginine IP6 coordination Lysine 492 +++ PO₄ contacting Lysine IP6 coordination Arginine 496 +++ JA-Ile and JAZ1 Arginine Auxin and contacting AUX/IAA binding Arginine 516 No Non Arginine IP6 coordination *Y2H assays were conducted with 10 μM COR in the medium. The strength of mutant COI1-JAZ9 interactions was scored relative to COI1-JAZ9 (designated as +++). ^(†)COI1 amino acids and their roles in the JAZ1-COI1-JA-Ile interaction. ^(‡)TIR1 amino acids corresponding to those in COI1 and roles in ligand-receptor interaction. ^(§)Additional COI1 amino acids selected for mutagenesis based on the crystal structure of the COI1-JAZ1 complex with COR or JA-Ile.

Y2H assays showed that 56% (18 of 32) of the alanine substitution mutants abolished COR-dependent interaction between COI1 and JAZ9 (FIG. 1A and Table 1). When the 18 residues were mapped to the crystal structure of the COI1-JAZ1 coreceptor, which became available after some of the earlier studies, 12 were found to make contacts with ligand, Ins(1,2,4,5,6)P5 (InsP5) or JAZ1 in the ligand-binding pocket. The crystal structure of COI1-JAZ1 coreceptor also shows several additional amino acids in the ligand-binding pocket, which could contribute to the interactions between COI1-ligand, COI1-JAZ, and COI1 interaction with InsP5 (Sheard et al., Nature 468(7322): 400-405 (2010)).

Ten additional amino acids were selected for site-directed mutagenesis to alanine (Table 1). Y2H assays showed that three alanine substitutions, Y302A, R326A, and Y444A, disrupted the COR-dependent COI1-JAZ9 interaction (FIG. 1B). As a result of such studies, a total of 21 COI1 residues were identified to be important for COR-induced formation of the COI1-JAZ coreceptor complex in yeast.

To determine whether substitutions that affected COR-dependent COI1-JAZ9 interaction could differentially affect JA-Ile-dependent COI1-JAZ9 interaction, quantitative liquid Y2H assays were conducted with COI11 mutants having one of ten alanine substitutions for the amino acids that directly contact JA-Ile (FIG. 2A-2B). These results show that: (i) seven alanine substitutions disrupted both JA-Ile-dependent and COR-dependent COI1-JAZ9 interaction, (ii) R409A substitution exhibited reduced COI1-JAZ9 interaction in the presence of JA-Ile or COR, and (iii) the R85A and R496A substitutions affect JAIle-dependent interaction more than COR-dependent interaction. No substitution was found to disrupt only COR-dependent interaction and still maintain JA-Ile-dependent COI1-JAZ9 interaction. However, none of the mutations disrupted only COR-dependent interaction but still maintained JAIle-dependent COI1-JAZ9 interaction (FIGS. 2A-2B).

These results show that COR is a remarkable mimic of JA-Ile and that most, if not all, of COI1 residues that are important for the action of JA-Ile are also important for COR action.

EXAMPLE 3 Structure-Guided Modeling of JA-Ile/COR Binding Sites in COI1

The initial mutagenesis described in Example 2 was based on alanine substitution of COI1 amino acids, which resulted in a reduction of the side-chain size for all of the amino acid residues targeted for mutagenesis, except for G357A. This Example describes experiments involving increasing the side-chain sizes of residues in COI1 that are in contact with JA-Ile/COR.

Although COR and JA-Ile are highly similar in structure, the flexibilities of COR and JA-Ile in the binding pocket are different. The structures of (3R,7S) JA-Ile and coronatine (COR) are shown below:

For example, the cyclohexene ring and the ethyl-cyclopropane group of COR appear more rigid than the equivalent parts (the pentenyl side-chain and the isoleucine side-chain, respectively) of JA-Ile (see, Sheard et al. Nature 468(7322):400-405 (2010)). In view of the foregoing results, the inventors hypothesized that the higher rigidity of the cyclohexene ring and the ethylcyclopropane group of COR may be more prone than the equivalent parts of JA-Ile to physical hindrance from an increased size of the amino acid side-chain with which COR/JA-Ile are in direct contact.

Based on such a hypothesis, COI1 residues A86 and A384 were viewed to be potential targets for mutagenesis for two reasons. First, in silico analysis of the putative JA-Ile binding pockets in diverse plant species for which the COI1 protein sequences are available revealed that, although most residues in the JA binding site are highly conserved across various taxa, residues at positions 86 and 384 exhibit a higher degree of polymorphism (FIG. 2E). In the moss species Physcomitrella patens, for example, isoleucine or valine occupy the corresponding position of A384 (FIG. 2E). Positions of A86 and A384 in Selaginella moellendorffii are replaced by isoleucine/valine and serine, respectively (FIG. 2E). Previous studies have shown that, although core JA signaling genes are found in P. palens (Wang et al. Plant Physiol 167(3):872-886 (2015)), neither JA nor JA-Ile could be detected in P. patens (Stumpe et al. New Phytol 188(3):740-749 (2010)). On the other hand, (9S, 13 S)-12-oxophytodienoic acid [cis-(+)-OPDA], which is the precursor of JA biosynthesis, is synthesized in P. patens, suggesting that P. patens may produce an alternative, OPDA-related ligand (Stumpe (2010)).

The inventors speculated that, during plant evolution, polymorphism(s) at positions 86 and 384 in the putative COI1 binding pocket may provide a basis for accommodating related ligands of distinct structural features. If so, mutations at these amino acid positions may produce differential effects on different ligands compared with more highly conserved residues, which are expected to affect different ligands similarly.

Second, in the JA-Ile/COR-binding pocket, the A86 and A384 residues make direct contacts with the ligand (FIG. 2E) and are situated close to the cyclohexene ring and the ethylcyclopropane group of COR or the equivalent parts of JA-Ile, the pentenyl side-chain, and the isoleucine side-chain, respectively (FIG. 3 panels A and B). The CB atom of A86 is 3.6 Å from the nearest C-atom in the pentenyl side-chain of JA-Ile and 3.7 Å from the ethyl group attached to the cyclohexene ring of COR in their respective crystal structures. The Cβ atom of A384 is 4.0 Å from the nearest C-atom of the isoleucine side chain of JA-Ile and 3.6 Å from the ethyl-cyclopropane group of COR. In silico mutagenesis followed by energy minimization revealed that the A384V substitution, in particular, would create steric clash with the isoleucine side-chain of JA-Ile or the ethyl group attached to the cyclopropane moiety of COR (FIG. 3 panels C and D). However, the flexibility of the isoleucine side-chain of JA-Ile would likely allow for its readjustment to fit the mutated ligand-binding pocket, whereas the rigidity of the ethyl-cyclopropane group of COR would not (FIG. 3 panels E and F).

Taken together, the in silico and structural modeling analyses indicate that mutating alanine to valine at position 384 may result in a ligand-binding pocket that is more unfavorable to the chemical structure of COR than that of JA-Ile.

EXAMPLE 4 Effects of Amino Acid Substitutions at Positions 86 and 384 on JA-Ile/COR-Dependent Formation of the COI1-JAZ9 Coreceptor

To test the hypothesis that mutating A384 or A86 may create a ligand-binding pocket that is more unfavorable to COR than to that of JA-Ile, these two alanine residues were first substituted with the corresponding residues found in lower plant species P. patens and S. moellendorffii (FIG. 2E). Specifically, the following COI1 mutants were generated: COI1A86I, COI1A86V, COI1A384I, COI1A384S, and COI1A384V.

Quantitative liquid Y2H assays revealed that both COI1A86I and COI1A86V abolished JA-Ile-dependent COI1-JAZ9 interaction, and reduced COR-dependent COI1-JAZ9 interaction (FIG. 4A). These results indicated that A86 may be needed for the action of both JA-Ile and COR, albeit more critical for JA-Ile than COR.

Substitutions at position 384 exhibited more diverse effects than those at position 86 on JA-Ile/COR-dependent COI1-JAZ9 interaction (FIG. 4A). COI1A384I disrupted both JA-Ile-dependent and COR-dependent interaction, whereas COI1A384S only reduced JA-Ile-dependent interaction. Most interestingly, COI1A384V greatly reduced COR-dependent interaction, but had less effect on JAIle-dependent COI1-JAZ9 interaction (FIG. 4A). As illustrated in FIG. 4B, 10 μM JA-Ile, which contains a mixture of active and inactive isomers of JA-Ile, was equivalent to 0.1 μM pure COR in promoting the COI1-JAZ9 interaction in yeast.

Seven additional substitutions at A384 were made to determine whether these substitutions would have an effect similar to that of COI1A384V. Of these seven substitutions (representing different types of side-chains), A384C reduced, and A384D, A384G, A384L, A384N, A384P, and A384T completely disrupted JA-Ile-dependent and COR-dependent interaction (FIG. 2C). In all, no additional substitutions affected COR-dependent COI1-JAZ9 interaction more than JA-Ile-dependent COI1-JAZ9 interaction.

Therefore, through extensive mutagenesis efforts a specific amino acid substitution, A384V, was identified in the JA-Ile binding pocket that preferably affects COR-dependent COI1-JAZ9 interaction, compared with JA-Ile-dependent COI1-JAZ9 interaction in yeast.

EXAMPLE 5 Transgenic Arabidopsis Plants Expressing COI1A384V are Fertile but Exhibit Differential Sensitivities to Methyl Jasmonate and COR In Vivo

To determine the physiological relevance of the results from Y2H assays, transgenic Arabidopsis plants (in COI1-30-null mutant background) were produced that express COI1A384V from the COI1 native promoter (pCOI1:COI1A384V-4×c-Myc; COI1A384V hereafter). As controls, transgenic lines were also generated that express wild type COI1 in the COI1-30-null background (pCOI1:COI1WT-4×c-Myc; COI1WT hereafter).

First, experiments were performed to determine whether COI1A384V complements the male sterile phenotype in COI1-30. JA is essential for male fertility and COI1 mutants are male sterile (Feys et al. Plant Cell 6(5):751-759 (1994)). Consistent with Y2H results showing that COI1A384V maintained substantial JA-Ile interaction, 83% of COI1A384V lines (10 of 12 lines analyzed) were fertile (FIG. 5A). Four fertile COI1A384V lines were randomly chosen for protein expression analysis and all were found to produce the c-Myc-tagged COI1A384V protein (FIG. 5B). No fertility penalty was detected in COI1A384V plants, as judged by the number of developed siliques and the number of seeds per silique, which are similar to wild-type plants (Table 2).

TABLE 2 Fertility of Col-0, COI1WT, COIA384V, and coil-30 plants No. of fertile No. of Plant flowers* seeds/silique^(†) Col-0 50/50 62 ± 4 coil-30/COI1^(WT) 50/50 57 ± 8 coil-30/COI1^(A384V) L1 50/50 58 ± 6 coil-30  0/50 0 No statistically significant differences were found by ANOVA (P = 0.411072) between Col-0, coil-30/COI1WT, and coil-30/COI1A384V L1. *Number of flowers that produce siliques/number of total flowers examined. Ten flowers of each plant and five plants of each genotype were examined. ^(†)Five siliques of each plant and a total of five plants were examined.

Next, COI1-JAZ9 pull-down experiments were performed to compare the responsiveness of plant-expressed COI1WT and COI1A384V proteins to serial concentrations of JA-Ile and COR using Escherichia coli-expressed JAZ9 protein, following the procedure reported by Katsir et al. (Proc Natl Acad Sci USA 105(19):7100-7105 (2008)). These experiments confirmed that a much higher (˜100-fold) concentration of COR was required for robust formation of the COI1A384V-JAZ9 co-receptor than for the COI1WT-JAZ9 co-receptor, whereas similar concentrations of JA-Ile were needed to promote the formation of the COI1A384V-JAZ9 and COI1WT-JAZ9 co-receptors (FIG. 4C). Hence, the modified COI1A384V protein does not form a complex with JAZ and COR, as readily as it complexes with JAZ and jasmonic acid (e.g., JA-Ile).

Further analyses were performed with two representative COI1A384V lines, L1 and L2, to determine their responses to JA-induced or COR-induced root growth inhibition. Dose-response experiments showed that the effect of 10 μM methyl jasmonate (MeJA), which is converted to the active form JA-Ile in planta, was equivalent to that of 0.2 μM COR in wild-type Col-0 plants (FIG. 5C). Unlike wild-type Col-0 plants, the root growth inhibition of COI1A384V plants was significantly less sensitive to 0.2 μM COR than to 10 μM MeJA (FIG. 5C). The potency of 0.2 μM COR in inhibiting root growth in COI1A384V plants was comparable to 0.1 μM MeJA, indicating that 0.2 μM COR was about 100-fold less effective in COI A384V than in Col-0 and COI1WT.

These results were consistent with the differential effects of the A384V substitution on JA-Ile-dependent vs. COR-dependent formation of the COI1-JAZ9 coreceptor observed in both Y2H and COI1-JAZ9 coreceptor pull-down assays. These results also confirmed that COI1A384V transgenic plants are differentially sensitive to MeJA vs. COR in vivo. COI A384V transgenic plants are thus more sensitive in vivo to MeJA than to COR.

EXAMPLE 6 Transgenic Arabidopsis Plants Expressing COI1A384V Exhibit Differential Expression of JA Response Marker Genes in Response to MeJA Vs. COR

Gene expression responses in COI1A384V transgenic plants were examined by evaluating the expression of the JA-responsive marker gene JAZ9 by quantitative PCR (qPCR).

As illustrated in FIG. 5D, JAZ9 gene expression was induced in Col-0 and COI1WT plants after application of MeJA or COR. In COI1A384V lines, however, JAZ9 gene expression in response to COR treatment was significantly reduced compared with Col-0 or COI1WT plants, whereas JAZ9 expressions in response to MeJA treatment was less affected in this same comparison (FIG. 5D). For example, in plants of the COI1A384V L1 line, MeJA treatment induced the expression of JAZ9 by 38-fold compared with that in COI1-30 (COI1-null mutant) plants. However, induction of JAZ9 gene expression in COI1A384VL1 was only eight-fold higher than that in COI1-30 plants after COR treatment.

These results indicate that the A384V substitution significantly affects the action of COR, while maintaining JA signaling required for substantial JA responses in gene expression.

The expression of SA-responsive genes PATHOGENESIS-RELATED GENE 1 (PR1) and SALICYLIC ACID INDUCTION DEFICIENT 2 (SID2) was examined in COI1A384V plants. As illustrated in FIGS. 5E-5F, expression of PR1 and SID2 genes was similarly low in Col-0, COI1WT and COI1A384V plants. These results indicate that the SA signaling pathway remained quiescent in COI1A384V plants, in a manner that was similar to SA signaling in Col-0 and COI1WT plants.

EXAMPLE 7 COI1A384V Transgenic Plants Gained Resistance to Pst DC3000 and Psm ES4326, while Maintaining High-Level Defense Against Chewing Insects

The data described above indicate that the inventors have succeeded in engineering a modified JA receptor that substantially uncouples endogenous hormone signaling from pathogen hijacking via COR. This Example describes experiments to test whether COI1A384V transgenic plants also gain resistance to COR-producing bacterial pathogens, while retaining substantial defense against chewing insects.

To test this possibility, bioassays were conducted using Pseudomonas syringae pv tomato (Pst) DC3000 and Pseudomona syringe pv maculicola (Psm) ES4326, two well-known COR-producing hemibiotrophic pathogens that infect Arabidopsis (Whalen et al. Plant Cell 3(1):49-59 (1991); Dong et al. Plant Cell 3(1):61-72 (1991)), and Spodoptera exigua, a generalist chewing insect that is susceptible to COI1-dependent defenses in Arabidopsis (Chung et al. Plant Physiol 146(3):952-964 (2008)).

Col-0 and COI1WT plants were highly susceptible to Pst DC3000 (FIG. 6A-6B). COI1A384V plants, however, exhibited significantly increased resistance to Pst DC3000, as evidenced by greatly reduced bacterial growth and disease symptoms (FIG. 6A-6B). Quantitatively, Pst DC3000 populations in COI1A384V lines were 254-fold to 42-fold lower than those in Col-0 plants and 189-fold to 31-fold lower than those in COI1WT transgenic plants (FIG. 6B). Similarly, COI1A384V plants exhibited significantly increased resistance to Psm ES4326 compared with wild-type Col-0 or COI1WT plants (FIG. 6C-6D). Control experiments showed that COI1-30 plants were highly resistant to both pathogens in these assays (FIGS. 6B and 6D).

Disease assays were conducted using Psi DC3118 and DB29, which are mutants of Pst DC3000 defective in COR production (Brooks et al. Mol Plant Microbe Interact 17(2):162-174 (2004); Zeng et al., PLoS Pathog 7(10): e1002291 (2011)). Similar levels of bacterial growth were observed in Col-0, COI1WT, and COI1A384V plants, indicating that the resistance gained in COI1A384V plants to Pst DC3000 was largely COR-dependent (FIG. 6E-6F).

Insect feeding assays were performed using S. exigua neonate larvae. As illustrated FIG. 7, S. exigua grew much more slowly on Col-0 plants than on COI1-30 mutant plants. The average weight of larvae feeding on COI1-30 plants was six-fold higher than larvae reared on COI1WT plants and five-fold higher than those grown on COI1A384V plants (FIG. 7A). Thus, COI1A384V plants maintained an almost wild-type levels of defense against S. exigua.

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All patents and publications referenced or mentioned herein are indicative of the levels of skill of those skilled in the art to which the invention pertains, and each such referenced patent or publication is hereby specifically incorporated by reference to the same extent as if it had been incorporated by reference in its entirety individually or set forth herein in its entirety. Applicants reserve the right to physically incorporate into this specification any and all materials and information from any such cited patents or publications.

The following statements are intended to describe and summarize various embodiments of the invention according to the foregoing description in the specification.

Statements:

-   -   1. A modified CORONATINE INSENSITIVE 1 (COI1) protein comprising         an amino acid sequence with at least one amino acid         substitution, replacement, deletion, or insertion relative to a         native (wild type) COI1 protein amino acid sequence that reduces         complex formation between coronatine and a JAZ repressor         protein.     -   2. The modified COI1 protein of statement 1, wherein the at         least one amino acid substitution, replacement, deletion, or         insertion is within a jasmonate binding pocket of the COI1         protein.     -   3. The modified COI1 protein of statement 1 or 2, wherein the at         least one amino acid substitution, replacement, deletion, or         insertion is not a direct contact jasmonate binding pocket of         the COI1 protein.     -   4. The modified COI1 protein of statement 1, 2, or 3, wherein         the native (wild type) COI1 protein is an Arabidopsis thaliana         protein, a Solanum lycopersicum protein, a Populus trichocarpa         protein, a Brachypodium distachyon protein, a Picea abies         protein, a Selaginella moellendorffii protein, a Physcomitrella         patens protein, a Brassicaceae protein, a grass protein, a         Lolium (ryegrass) protein, a Glycine max protein, a Zea mays         protein, a Triticum spp. protein, a Brassica rapa protein, a         Brassica napus protein, a Triticum aestivum plant, a Populus         trichocarpa plant, an Arachis hypogaeal plant, or a         Physcomitrella patens plant.     -   5. The modified COI1 protein of statement 1-3 or 4, wherein the         modified COI1 protein is a modified Arabidopsis thaliana         protein, a Solanum lycopersicum protein, a Populus trichocarpa         protein, a Brachypodium distachyon protein, a Picea abies         protein, a Selaginella moellendorffii protein, a Physcomitrella         patens protein, a Brassicaceae protein, a grass protein, a         Lolium (ryegrass) protein, a Glycine max protein, a Zea mays         protein, a Triticum spp. protein, a Brassica rapa protein, a         Brassica napus protein, a Triticum aestivum plant, a Populus         trichocarpa plant, an Arachis hypogaeal plant, or a         Physcomitrella patens plant.     -   6. The modified COI1 protein of statements 1-4 or 5, wherein the         modified COI1 protein has a hydrophobic amino acid that is not         alanine at the position of an alanine in the native (wild type)         COI1 protein.     -   7. The modified COI1 protein of statements 1-5 or 6, wherein the         modified COI1 protein has at least one amino acid substitution         within about 0-10 amino acid positions of amino acid position         384 where the amino acid that is replaced in the native (wild         type) COI1 protein is an alanine, and the replacement is a         hydrophobic amino acid.     -   8. The modified COI1 protein of statements 1-6 or 7, wherein the         modified COI1 protein has an A384V (alanine at position 384         replaced by a valine).     -   9. The modified COI1 protein of statement 1-7 or 8, with greater         binding affinity for jasmonate, methyljasmonate, or         jasmonate-Ile, than for a plant toxin that forms a complex with         a wild type (native) COIL protein and a JAZ protein.     -   10. The modified COI1 protein of statement 1-8 or 9, which binds         jasmonate, methyljasmonate, or jasmonate-Ile with greater         affinity than it binds a plant toxin produced by Pseudomonas         syringae pv tomato, Pseudomonas syringae pv maculicola,         Pseudomonas syringe pv atropurpurea, Pseudomonas syringae pv         glycinea, Pseudomonas syringae pv morsprunorum, Pseudomonas         syringae pv porri, Pseudomonas cannabina pv alisalensis,         Streptomyces scabies, Xanthomonas campestris pv phormiicola,         Pseudomonas savastanoi pv glycinea, Pectobacterium atrosepticum         (syn. Erwinia carotovora subsp. atroseptica, or Nectria sp.         DA060097.     -   11. The modified COI1 protein of statement 1-9 or 10, with         greater binding affinity for jasmonate, methyljasmonate, or         jasmonate-Ile, than for coronatine or cinnacidin.     -   12. The modified COI1 protein of statement 1-10 or 11, with         greater binding affinity for jasmonate, methyljasmonate, or         jasmonate-Ile, than for a compound of formula I:

wherein:

-   -   -   R₁ can be a three to six carbon (C₃ to C₆) alkyl that can             have one double bond, or R₁ can be a C₃ to C₆ alkylene that             can have one double bond and that links to R₂ to form a             cycloalkyl ring;         -   R₂ can be a CH₂ or a CH;         -   A is a cyclopentyl ring;         -   B can be a C₃ to C₆ cycloalkyl ring or a heterocycloalkyl             ring; and         -   R₃ can be a C₁ to C₃ alkyl; and         -   R₄ can be hydrogen or C₁ to C₃ alkyl.

    -   13. The modified COI1 protein of statement 1-11 or 12, wherein         at least 10-fold, or at least 20-fold, or at least 30-fold, or         at least 40-fold, or at least 50-fold, or at least 60-fold, or         at least 70-fold, at least 75-fold, at least 80-fold, at least         85-fold, at least 90-fold, or at least 95-fold, at least         100-fold, at least 110, or at least 125-fold, at least 150-fold,         or at least 175-fold higher concentration of coronatine,         cinnacidin, or a compound of formula I is required for formation         of the COI1A384V-JAZ9 co-receptor than for the COI1WT-JAZ9         co-receptor.

    -   14. The modified COI1 protein of statement 1-12 or 13, wherein         treatment with methyljasmonate induces expression of JAZ9 in         cells expressing the modified COI1 protein by at least 10-fold,         by at least 15-fold, by at least 20-fold, by at least 25-fold,         by at least 30-fold, by at least 35-fold, at least 40-fold, or         at least 50-fold compared with that in COI1-30 (COI1-null         mutant) plants.

    -   15. The modified COI1 protein of statement 1-13 or 14, wherein         treatment with coronatine or a compound of formula I induces         expression of JAZ9 in cells expressing the modified COI1 protein         by less than 10-fold, or by less than 9-fold, or by about 8-fold         than COI1-30 plants after COR treatment or treatment with a         compound of formula I.

    -   16. The modified COI1 protein of statement 1-14 or 15, wherein         plants expressing the modified protein have increased resistance         to bacteria compared to parental or wild type plants under the         same conditions.

    -   17. The modified COI1 protein of statement 1-15 or 16, wherein         plants expressing the modified protein have increased resistance         to Pseudomonas syringae pv tomato (Pst) DC3000 and/or         Pseudomonas syringae pv maculicola (Psm) ES4326 bacteria         compared to parental or wild type plants under the same         conditions.

    -   18. The modified COI1 protein of statement 1-16 or 17, wherein         plants expressing the modified protein have at least 10-fold, or         at least 15-fold, or at least 20-fold, or at least 25-fold, or         at least 30-fold, or at least 35-fold, or at least 40-fold, or         at least 45-fold, or at least 50-fold, or at least 60-fold, or         at least 75-fold, or at least 100-fold, or at least 150-fold, or         at least 200-fold, or at least 250-fold fewer Pseudomonas         syringae pv tomato (Pst) DC3000 and/or Pseudomonas syringae pv         maculicola (Psm) ES4326 bacteria compared to parental or wild         type plants under the same conditions.

    -   19. The modified COI1 protein of statement 1-17 or 18, wherein         plants expressing the modified protein retain insect resistance         similar to plants expressing wild type or unmodified COI1.

    -   20. The modified COI1 protein of statement 1-8 or 19, wherein         plants expressing the modified protein have at least 2-fold, or         at least 3-fold, or at least 4-fold, or at least 5-fold less         insect Spodoptera exigua larvae by weight than COI1-30 plants.

    -   21. The modified COI1 protein of statement 1-19 or 20, which         when expressed in plants exhibits at least 2-fold, at least         5-fold, at least 10-fold, at least 25-fold, at least 50-fold, at         least 75-fold, at least 90-fold, at least 100-fold less         inhibition of root growth in the presence of coronatine or a         compound of formula I, than an unmodified parental or wild type         COI1 protein expressed in a plant under the same conditions.

    -   22. The modified COI1 protein of statement 1-20 or 21, wherein         root growth is inhibited in a plant expressing an unmodified         parental or wild type COI1 protein of by at least 2-fold, at         least 5-fold, at least 10-fold, at least 25-fold, at least         50-fold, at least 75-fold, at least 90-fold, at least 100-fold         greater than root growth is inhibited in a plant expressing the         modified COI1 protein under the same conditions, where the         conditions comprise contacting the plant with coronatine or a         compound of formula I.

    -   23. The modified COI1 protein of statement 1-21 or 22, wherein a         plant expressing the modified COI1 protein is fertile.

    -   24. The modified COI1 protein of statement 1-22 or 23, wherein         at least 50%, or at least 60%, or at least 70%, or at least 75%,         or at least 80%, or at least 85%, or at least 90%, or at least         95% of plants in a population of plants expressing the modified         COI1 protein are fertile.

    -   25. The modified COI1 protein of statement 1-23 or 24, with an         amino acid substitution, replacement, or deletion at a position         equivalent to position 384 of a SEQ ID NO:1 COI1 protein.

    -   26. The modified COI1 protein of statement 1-24 or 25, with an         amino acid sequence that has at least 90%, or at least 95%, or         at least 96%, or at least 97%, at least 98%, or at least 99%/0         sequence identity to SEQ ID NO:1, 2, 5, 8, 10, 13, 16, 19, 22,         25, 28, 31, 33, 36, 39, 42, 45, or 48.

    -   27. A transgene or expression cassette comprising a promoter         operably linked to a nucleic acid segment encoding the modified         COI1 protein of statement 1-24 or 25.

    -   28. The transgene or expression cassette of statement 27,         wherein the promoter is an endogenous COI1 promoter operably         linked to the nucleic acid segment encoding the modified COI1         protein.

    -   29. The transgene or expression cassette of statement 27 or 28,         wherein the promoter is heterologous to the nucleic acid segment         encoding the modified COI1 protein.

    -   30. A cell comprising the transgene or expression cassette of         statement 27, 28, or 29.

    -   31. The cell of statement 30, which is a plant cell.

    -   32. The cell of statement 30 or 31 which is a monocotyledon or         dicotyledon cell.

    -   33. The cell of statement 30, 31, or 32, which is a Brassicaceae         or other Solanaceae cell.

    -   34. The cell of statement 30-32 or 33, which is an alfalfa,         forage legume alfalfa, algae, apple, avocado, balsam, barley,         broccoli, Brussels sprout, cabbage, canola, cassava,         cauliflower, cocoa, cole vegetable, collard, corn, cottonwood,         crucifers, earthmoss, grain legumes, grass, forage grass,         jatropa, kale, kohlrabi, maize, miscanthus, moss, mustard, nut,         nut sedge, oat, oil firewood trees, oilseed, peach, peanut,         potato, radish, rape, rapeseed, rice, rutabaga, sorghum,         soybean, sugar beet, sugarcane, sunflower, switchgrass, tobacco,         tomato, turnip, or wheat cell.

    -   35. A plant comprising the cell of statement 30-33 or 34.

    -   36. The plant of statement 35, which has increased resistance to         bacteria compared to parental or wild type plants under the same         conditions.

    -   37. The plant of statement 35 or 36, which has increased         resistance to Pseudomonas syringae pv tomato (Psi) DC3000 and/or         Pseudomonas syringae pv maculicola (Psm) ES4326 bacteria         compared to parental or wild type plants under the same         conditions.

    -   38. The plant of statement 35, 36, or 37, which has at least         10-fold, or at least 15-fold, or at least 20-fold, or at least         25-fold, or at least 30-fold, or at least 35-fold, or at least         40-fold, or at least 45-fold, or at least 50-fold, or at least         60-fold, or at least 75-fold, or at least 100-fold, or at least         150-fold, or at least 200-fold, or at least 250-fold fewer         Pseudomonas syringae pv tomato (Pst) DC3000 and/or Pseudomonas         syringae pv maculicola (Psm) ES4326 bacteria compared to         parental or wild type plants under the same conditions.

    -   39. The plant of statement 35-37 or 38 which has at least         2-fold, or at least 3-fold, or at least 4-fold, or at least         5-fold fewer insect Spodoptera exigua larvae by weight than         COI1-30 plants under the same conditions.

    -   40. The plant of statement 35-38 or 39, which has at least         2-fold, at least 5-fold, at least 10-fold, at least 25-fold, at         least 50-fold, at least 75-fold, at least 90-fold, at least         100-fold less inhibition of root growth in the presence of         coronatine or a compound of formula I, than an unmodified         parental or wild type COI1 protein expressed in a plant under         the same conditions, where the conditions comprise contacting         the plant with coronatine or a compound of formula I.

    -   41. The plant of statement 35-39 or 40, wherein root growth is         inhibited in a plant expressing an unmodified parental or wild         type COI1 protein by at least 2-fold, at least 5-fold, at least         10-fold, at least 25-fold, at least 50-fold, at least 75-fold,         at least 90-fold, at least 100-fold greater than root growth is         inhibited in a plant expressing the modified COI1 protein under         the same conditions, where the conditions comprise contacting         the plant with coronatine or a compound of formula I.

    -   42. The plant of statement 35-40 or 41, which is fertile.

    -   43. The plant of statement 35-41 or 42, wherein at least 50%, or         at least 60%, or at least 70%, or at least 75%, or at least 80%,         or at least 85%, or at least 90%, or at least 95% of plants are         fertile in a population of plants expressing the modified COI1         protein.

    -   44. A method comprising applying a herbicide to a crop         comprising the plant of statement 35-42 or 43 to kill or inhibit         growth of plants that do not express the modified COI1 protein.

    -   45. The method of statement 44, wherein the herbicide is a         compound of formula I:

wherein:

-   -   -   R₁ can be a three to six carbon (C₃ to C₆) alkyl that can             have one double bond, or R₁ can be a C₃ to C₆ alkylene that             can have one double bond and that links to R₂ to form a             cycloalkyl ring;         -   R₂ can be a CH₂ or a CH;         -   A is a cyclopentyl ring;         -   B can be a C₃ to C₆ cycloalkyl ring or a heterocycloalkyl             ring; and         -   R₃ can be a C₁ to C₃ alkyl; and         -   R₄ can be hydrogen or C₁ to C₃ alkyl.

    -   46. The method of statement 44 or 45, wherein the herbicide is         coronatine.

    -   47. The method of statement 44, wherein the herbicide is         cinnacidin.

    -   48. The method of statement 44, wherein the herbicide is a         cinnacidin analog selected from compound 2 and 11 shown below:

-   -   49. The method of statement 44-47 or 48, wherein a herbicidally         effective amount of the herbicide is applied.     -   50. The method of statement 49, wherein the herbicidally         effective amount of the herbicide is at least 50 g per hectacre,         at least 100 g per hectacre, at least 125 g per hectacre, at         least 150 g per hectacre, at least 200 g per hectacre, at least         250 g per hectacre, at least 300 g per hectacre, at least 400 g         per hectacre, at least 500 g per hectacre, at least 700 g per         hectacre, at least 1000 g per hectacre, at least 1500 g per         hectacre, or at least 2000 g per hectacre.     -   51. The method of statement 49 or 50, wherein the herbicidally         effective amount of the herbicide is less than 2500 g per         hectacre, or less than 2000 g per hectacre, or less than 1500 g         per hectacre, or less than 1000 g per hectacre.     -   52. The method of statement 44-50 or 51, wherein the crop         comprises seedlings.     -   53. The method of statement 44-51 or 52, wherein the crop         comprises a seeded field.     -   54. The method of statement 44-52 or 53, further comprising         planting seeds comprising the transgene or expression cassette         of statement 27, 28, or 29 to provide the crop.     -   55. The method of statement 44-53 or 54, further comprising         planting seeds comprising a modified COI1 gene that encodes the         modified protein.

The specific products, compositions, and methods described herein are representative, exemplary and not intended as limitations on the scope of the invention. Other objects, aspects, and embodiments will occur to those skilled in the art upon consideration of this specification, and are encompassed within the spirit of the invention as defined by the scope of the claims. It will be readily apparent to one skilled in the art that varying substitutions and modifications may be made to the invention disclosed herein without departing from the scope and spirit of the invention. The terms and expressions that have been employed are used as terms of description and not of limitation, and there is no intent in the use of such terms and expressions to exclude any equivalent of the features shown and described or portions thereof, but it is recognized that various modifications are possible within the scope of the invention as claimed. Thus, it will be understood that although the present invention has been specifically disclosed by embodiments and optional features, modification and variation of the concepts herein disclosed may be resorted to by those skilled in the art, and that such modifications and variations are considered to be within the scope of this invention as defined by the appended claims and statements of the invention.

The invention illustratively described herein may be practiced in the absence of any element or elements, or limitation or limitations, which is not specifically disclosed herein as essential. The methods and processes illustratively described herein may be practiced in differing orders of steps, and the methods and processes are not necessarily restricted to the orders of steps indicated herein or in the claims.

As used herein and in the appended claims, the singular forms “a,” “an,” and “the” include plural reference unless the context clearly dictates otherwise. Thus, for example, a reference to “a plant” or “a seed” or “a cell” includes a plurality of such plants, seeds or cells, and so forth. In this document, the term “or” is used to refer to a nonexclusive or, such that “A or B” includes “A but not B,” “B but not A,” and “A and B,” unless otherwise indicated.

Under no circumstances may the patent be interpreted to be limited to the specific examples or embodiments or methods specifically disclosed herein. Under no circumstances may the patent be interpreted to be limited by any statement made by any Examiner or any other official or employee of the Patent and Trademark Office unless such statement is specifically and without qualification or reservation expressly adopted in a responsive writing by Applicants.

The invention has been described broadly and generically herein. Each of the narrower species and subgeneric groupings falling within the generic disclosure also form part of the invention. This includes the generic description of the invention with a proviso or negative limitation removing any subject matter from the genus, regardless of whether or not the excised material is specifically recited herein. In addition, where features or aspects of the invention are described in terms of Markush groups, those skilled in the art will recognize that the invention is also thereby described in terms of any individual member or subgroup of members of the Markush group. 

What is claimed:
 1. A modified CORONATINE INSENSITIVE 1 (COI1) protein comprising an amino acid sequence with at least one amino acid substitution or replacement at a position equivalent to position 384 of a SEQ ID NO: 1 COI1 protein, which is within a jasmonate binding pocket of the COI1 protein, wherein the at least one amino acid substitution reduces complex formation between the modified COI1 protein, coronatine, and a JAZ repressor protein compared to the native (wild types) COI1 protein.
 2. The modified COI1 protein of claim 1, wherein the modified COI1 protein has a hydrophobic amino acid that is not alanine at the position of an alanine in the native (wild type) COI1 protein.
 3. The modified COI1 protein of claim 1, wherein the modified COI1 protein has at least one amino acid substitution within about 0-10 amino acid positions of amino acid position 384 where the amino acid that is replaced in the native (wild type) COI1 protein is an alanine, and the replacement is a hydrophobic amino acid.
 4. The modified COI1 protein of claim 1, wherein the modified COI1 protein has a valine substitution or replacement at a position equivalent to position 384 of SEQ ID NO:1.
 5. The modified COI1 protein of claim 1, with greater binding affinity for jasmonate, methyljasmonate, or jasmonate-Ile, than for a plant toxin that forms a complex with a wild type (native) COI1 protein and a JAZ protein.
 6. The modified COI1 protein of claim 1, which binds jasmonate, methyljasmonate, or jasmonate-Ile with greater affinity than it binds a plant toxin produced by Pseudomonas syringaepv tomato, Pseudomonas syringae pv maculicola, Pseudomonas syringae pv atropurpurea, Pseudomonas syringae pv glycinea, Pseudomonas syringae pv morsprunorum, Pseudomonas syringaepv porri, Pseudomonas cannabina pv alisalensis, Streptomyces scabies, Xanthomonas campestris pv phormiicola, Pseudomonas savastanoi pv glycinea, Pectobacterium atrosepticum(syn. Erwinia carotovora subsp. atroseptica, or Nectria sp. DA060097.
 7. The modified COI1 protein of claim 1, with greater binding affinity for jasmona methyljasmonate, or jasmonate-Ile, than for a compound of formula I:

wherein: R₁ can be a three to six carbon (C₃ to C₆ )alkyl that can have one double bond, or R₁ can be a C₃ to C₆ alkylene that can have one double bond and that links to R₂ to form a cycloalkyl ring; R₂ can be a CH₂ or a CH; A is a cyclopentyl ring; B can be a C₃ to C₆ cycloalkyl ring or a heterocycloalkyl ring; and R₃ can be a C₁ to C₃ alkyl; and R₄ can be hydrogen or C₁ to C₃ alkyl.
 8. The modified COI1 protein of claim 7, wherein at least 10-fold higher concentration of coronatirie, cinnacidin, or a compound of formula I is required for formation of a COI1 A 384V-JAZ9 co-receptor in the presence of the coronatine, cinnacidin, or a compound of formula I, than for a COI1WT-JAZ9 co-receptor in the presence of coronatine, cinnacidin, or a compound of formula I.
 9. The modified COI1 protein of claim 1, wherein plants expressing the modified protein have increased resistance to bacteria compared to parental or wild type plants under the same conditions.
 10. The modified COI1 protein of claim 1, wherein plants expressing the modified protein have increased resistance to Pseudomonas syringae pv tomato (Pst) DC3000 and/or Pseudomonas syringae pv maculicola (Psm) ES4326 bacteria compared to parental or wild type plants under the same conditions.
 11. The modified COI1 protein of claim 1, wherein plants expressing the modified protein have at least 10-fold fewer Pseudomonas syringae pv tomato (Pst) DC3000 and/or Pseudomonas syringae pv maculicola (Psm) ES4326 bacteria compared to parental or wild type plants under the same conditions.
 12. The modified COI1 protein of claim 1, wherein plants expressing the modified protein retain insect resistance of plants expressing wild type or unmodified COI1, or have increased insect resistance compared to plants expressing (native) wild type or unmodified COI1.
 13. The modified COI1 protein of claim 1, wherein plants expressing the modified protein have at least 2-fold less insect Spodoptera exigua larvae by weight than coil-30 plants.
 14. The modified COI1 protein of claim 1, wherein plants expressing the modified protein exhibit at least 2-fold less inhibition of root growth in the presence of coronatine or a compound of formula I, than an unmodified parental or wild type COI1 protein exhibits in a plan under the same conditions.
 15. The modified COI1 protein of claim 1, with an amino acid sequence that has at least 95% sequence identity to SEQ ID NO: 2, 5, 8, 10, 13, 16, 19, 22, 25, 28, 31, 33, 36, 39, 42, 45, or
 48. 16. A cell comprising modified COI1 protein of claim
 1. 17. The cell of claim 16, which is an alfalfa, forage legume alfalfa, algae, apple, avocado, balsam, barley, broccoli, Brussels sprout, cabbage, canola, cassava, cauliflower, cocoa, cote vegetable, collard, corn, cottonwood, crucifers, earthmoss, grain legumes, grass, forage grass, jatropa, kale, kohlrabi, maize, miscanthus, moss, mustard, nut, nut sedge, oat, oil firewood trees, oilseed, peach, peanut, potato, radish, rape, rapeseed, rice, rutabaga, sorghum, soybean, sugar beet, sugarcane, sunflower, switchgrass, tobacco, tomato, turnip, or wheat cell.
 18. A transgene or expression cassette comprising a promoter operably linked to a nucleic acid segment encoding the modified COI1 protein of claim
 1. 19. The transgene or expression cassette of claim 18, wherein the promoter is an endogenous COI1 promoter operably linked to the nucleic acid segment encoding the modified COI1 protein.
 20. The transgene or expression cassette of claim 18, wherein the promoter is heterologous to the nucleic acid segment encoding the modified COI1 protein.
 21. A plant comprising the modified COI1 protein of claim
 1. 22. The plant of claim 21, which has at least 10-fold increased resistance to Pseudomonas syringaepv tomato (Pst) DC3000 and/or Pseudomonas syringae pv maculicola (Psm) ES4326 bacteria compared to parental or wild type plants under the same conditions.
 23. The plant of claim 21, which has at least 2-fold fewer Spodoptera exigua larvae by weight than coil-30 plants under the same conditions.
 24. The plant of claim 21, which has at least 2-fold less inhibition of root growth in the presence of coronatine or a compound of formula I, than an unmodified parental or wild type COI1 protein expressed in a plant under the same conditions, where the conditions comprise contacting the plant with coronatine or a compound of formula I:

wherein: R₁ can be a three to six carbon (C₃ to C₆) alkyl that can have one double bond, or R₁ can be a C₃ to C₆ alkylene that can have one double bond and that links to R₂ to form a cycloalkyl ring; R₂ can be a CH₂ or a CH; A is a cyclopentyl ring; B can be a C₃ to C₆ cycloalkyl ring or a heterocycloalkyl ring; and R₃ can be a C₁ to C₃ alkyl; and R₄ can be hydrogen or C₁ to C₃ alkyl.
 25. The plant of claim 21, which is fertile.
 26. A method comprising applying a herbicide composition comprisil coronatine to a crop comprising one or more plants expressing a modified COI1 protein to kill or inhibit growth of plants that do not express the modified COI1 protein, wherein the modified COI1 protein comprises an amino acid sequence with at least one amino acid substitution or replacement at a position equivalent to position 384 of a SEQ ID NO: 1 COI1 protein, which is within a jasmonate binding pocket of the COI1 protein, wherein the at least one amino acid substitution reduces complex formation between coronatine and a JAZ repressor protein.
 27. The method of claim 26, wherein the plant expressing the modified COI1 protein grows in the presence of the herbicide.
 28. The method of claim 26, wherein plant expressing a modified COI1 protein is fertile. 